Mercurial > repos > marcel > caddsuite_mac10_6

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/AntitargetRescorer	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/AntitargetRescorer.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/AutoModel	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/AutoModel.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/BindingDBCleaner	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/BindingDBCleaner.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/CADDSuite-description.txt	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,60 @@
+This package contains tools belonging to
+CADDSuite: A flexible and open framework for Computer-Aided Drug Design
+
+There are tools for the following tasks:
+
+Get Data:
+	- CombiLibGenerator: generate R-group decorated ligands
+	- DBExporter: fetch (filtered) molecules from DB
+
+Preparation of input:
+	- PDBCutter: separate ligand and receptor
+	- ProteinProtonator: protonate protein structures
+	- BindingDBCleaner: fix data from bindingdb.org
+	- EvenSplit: generate splits w/ equal property range
+	- PropertyModifier: modify property tags
+	- LigandFileSplitter: split molecule files
+	- Ligand3DGenerator: generate 3D coordinates for small molecules
+
+Structure checks and evaluations:
+	- ProteinCheck: evaluate protein quality
+	- LigCheck: chemical sanity check for ligands
+
+QuEasy (QSAR):
+	- InputReader: read molecules and generate features
+	- ModelCreator: create a QSAR model
+	- FeatureSelector: automatically select features of a QSAR model
+	- Validator: evaluate quality of a QSAR model
+	- MolPredictor: predict molecule activities with QSAR model
+	- AutoModel: automatically find best QSAR model
+
+Docking:
+	- WaterFinder: find strongly bound water molecules
+	- SpatialConstraintDefiner: define spatial constraint
+	- ConstraintsFinder: find strongly interacting residues
+	- PocketDetector: detect ligand binding pocket
+	- GridBuilder: precalculate grids for docking
+	- IMeedyDock: run Iterative Multi-Greedy Docking
+
+Rescoring:
+	- SimpleRescorer: rescore docking results
+	- TaGRes-train: Target-specific Grid-Rescoring, training
+	- TaGRes: Target-specific Grid-Rescoring
+	- AntitargetRescoring: rescore w/ respect to antitarget
+
+Analysis:
+	- ScoreAnalyzer: generate ROC or enrichment plots
+	- SimilarityAnalyzer: analyze similarity between two molecule sets
+	- PropertyPlotter: plot molecule properties
+	- RMSDCalculator: calculate RMSD between conformations
+	- VendorFinder: search vendors for compounds
+
+Convert, combine and store:
+	- DockResultMerger: merge docking output files and/or filter them
+	- MolCombine: combine molecular files
+	- DBImporter: import molecules into DB
+	- Converter: interconvert molecular file-formats
+	- MolDepict: generate structure diagrams
+	- VendorFinder: search vendors for compounds
+
+For more information about an individual tool, please call the tool without any parameters (or with '-help').
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/CombiLibGenerator	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/CombiLibGenerator.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ConstraintsFinder	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/ConstraintsFinder.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Converter	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/Converter.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/DBExporter	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/DBExporter.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/DBImporter	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/DBImporter.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/DockResultMerger	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/DockResultMerger.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/EvenSplit	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/EvenSplit.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/FeatureSelector	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/FeatureSelector.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/GalaxyConfigGenerator	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/GalaxyConfigGenerator.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/GridBuilder	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/GridBuilder.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/IMGDock	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/IMGDock.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/InputPartitioner	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/InputPartitioner.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/InputReader	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/InputReader.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/InteractionConstraintDefiner	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/InteractionConstraintDefiner.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/LigCheck	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/LigCheck.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Ligand3DGenerator	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/Ligand3DGenerator.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/LigandFileSplitter	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/LigandFileSplitter.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ModelCreator	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/ModelCreator.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolCombine	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/MolCombine.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolDepict	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/MolDepict.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolFilter	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/MolFilter.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolPredictor	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/MolPredictor.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PDBCutter	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/PDBCutter.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PDBDownload	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/PDBDownload.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PartialChargesCopy	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/PartialChargesCopy.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PocketDetector	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/PocketDetector.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Predictor	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/Predictor.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PropertyModifier	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/PropertyModifier.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PropertyPlotter	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/PropertyPlotter.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ProteinCheck	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/ProteinCheck.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ProteinProtonator	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/ProteinProtonator.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/QuEasyRun	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/QuEasyRun.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/README	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,41 @@
+-----------------------------------------------------------------------
+   CADDSuite - A flexible and open framework and workflow system
+               for computer-aided drug design
+-----------------------------------------------------------------------
+
+This package contains all tools belonging to CADDSuite.
+For an overview over the contained tools, please see CADDSuite-description.txt.
+After extraction the package, you can directly start the applications using the startup-scripts in the base-folder.
+
+For more information about an individual tool, please call the tool without any parameters (or with '-h').
+
+
+
+--------------------------------------------------------------------
+Instructions for integration of CADDSuite into the workflow-system
+Galaxy (http://getgalaxy.org)
+--------------------------------------------------------------------
+
+
+In order to install CADDSuite into your Galaxy installation, please to the following:
+
+Let's assume $galaxybase is the base-folder of your Galaxy installation.
+If you don't have a galaxy-installation yet, download a version from http://getgalaxy.org and follow the installation instructions shown there first.
+
+
+-- Extract the CADDSuite archive into a new folder $galaxybase/tools/CADDSuite, or extract it somewhere else and create a link named $galaxybase/tools/CADDSuite that points to this destination.
+
+After this, you need to copy a few files that you find in the galaxyconfig/ subfolder of this archive to the destinations specified below:
+
+-- Copy tool_conf.xml and datatypes_conf.xml to $galaxybase if you want to setup your Galaxy instance for exclusive use of CADDSuite, or copy the contents of those files into the files already existing in $galaxybase if you want to keep using tools that came along with the Galaxy installation.
+
+-- Copy molFiles.py, confFiles.py and countResidues.sh to $galaxybase/lib/galaxy/datatypes/
+
+-- Add "#import molFiles, confFiles.py" to the beginning of the file $galaxybase/lib/galaxy/datatypes/registry.py
+
+
+
+Last but not least, restart Galaxy.
+All CADDSuite tools should now appear in your Galaxy webinterface.
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/RMSDCalculator	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/RMSDCalculator.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ScoreAnalyzer	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/ScoreAnalyzer.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SideChainGridBuilder	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/SideChainGridBuilder.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SimilarityAnalyzer	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/SimilarityAnalyzer.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SimpleRescorer	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/SimpleRescorer.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SpatialConstraintDefiner	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/SpatialConstraintDefiner.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/TaGRes	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/TaGRes.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/TaGRes-train	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/TaGRes-train.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Validator	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/Validator.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/VendorFinder	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/VendorFinder.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/WaterFinder	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/WaterFinder.bin "$@"
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/changelog.txt	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,46 @@
+Version 0.94, 06-27-2011:
+	- Fixed tool-startup script for pathes containing whitespaces
+	- New tool SpatialConstraintDefiner
+	- New tool InteractionConstraintDefiner
+	- Removed superficial pathes from startup-script
+	- Slight change in ParamFile format (i.e. the files written with -write_par)
+	- Renamed IMeedyDock to IMGDock
+
+Version 0.93, 05-30-2011:
+	- Split Rescorer into 3 tools: SimpleRescorer, TaGRes-train, TaGRes (Target-Specific Grid-Rescoring)
+	- Allow to optionally specify output filenames to LigandFileSplitter
+	- Fixed creation of galaxy-scripts for tools with inputfile-lists
+	- Fixed creation of galaxy-scripts for Converter and DockResultMerger
+	- Automatically create and add all files necessary for integration of CADDSuite into Galaxy to the makeself archive
+	- New tool MolFilter
+	- Fixed some gnuplot issues
+	- Added PDBDownload tool
+	- Slight change of format of ParamFile
+	- Added some missing tool-manuals
+	- Disable B-factor check for hydrogens in ProteinCheck
+	- Added safeguards to several tools
+	- Automatically delete existing hydrogens from BALL-system before protonation is done by ProteinProtonator
+	- Fixed reading of mulitple ScoreGridSets (for cases when no ini-file is used)
+	- Simplified use of VendorFinder by allowing to set all db-parameters on the command-line (instead of using ini-file)
+	- Enhanced several tool manuals
+	- Let tools register their category (e.g. Preparation, Docking, etc.). Write and read information about this category to/from ParamFiles.
+
+Version 0.92, 05-17-2011:
+	- Speed-up of ob-mol generation
+	- Support build on Windows
+	- ProteinCheck now generates protein-quality report as pdf
+	- Added info about mandatory parameters and parameter-restrictions to parameter xml-file
+	- Simplified use of DBImporter+DBExporter by allowing to set all db-parameters on the command-line (instead of using ini-file)
+	- Simplified use of some other tools by merging several flags into one string-parameter that has restrictions.
+	- New tool MolDepict. It generates structure diagrams for small molecules by using openbabel's svg-writer and merges them to one pdf-file (3 on 5).
+	- Allow to create makeself-archive containing CADDSuite, all necessary contrib-libs, data-files and install-script
+	- Write information about supported file-formats to parameter xml-file
+	- new tool ProteinProtonator
+	- new tool Ligand3DGenerator
+	- new tool GalaxyConfigGenerator
+	- allow to open file that do not have an extension (by searching for format-specific keywords)
+
+Version 0.91, 04-12-2011:
+	- All tools now write a manual text to cout as well as to parameter xml-file (as generated by 'write_par)
+
+Version 0.9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/Amber/amber96-docking.ini	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,1666 @@
+; This file contains parameter needed for nonbonded ScoringComponents.
+; The parameters were converted from parm96.dat using amber2ini and all sections for bonded parameters were removed since are not needed for docking.
+; Furthermore, lennard-jones and AtomType parameters for some metal ions were obtained from the sources indicated in the comment column and added to this file.
+
+[Options]
+key:0
+@SCEE=1.2
+; please check the settings for SCEE! AMBER91/89a requires a value of 2.0 here!
+
+
+
+
+[HydrophilicTypes]
+; ignored
+;
+C   H   HO  N   NA  NB  NC  N2  NT  N2  N3  N*  O   OH  OS  P   O2
+
+
+[HydrogenBonds]
+ver:version key:I key:J value:A value:B
+@unit_A=kcal/mol*A^12
+@unit_B=kcal/mol*A^10
+;
+;
+;  Rev  I   J      A          B
+;  --- --- --- ---------- ----------
+   1.0  HW OW     0.0000     0.0000
+
+
+[AtomTypes]
+value:ver key:type value:mass value:comment
+@unit=g/mol
+;
+;
+;   Rev Type    mass      comment
+;   --- ---- ---------- ----------------------------------
+    1.0  BR    79.90000 "bromine"
+    1.0  C     12.01000 "sp2 C carbonyl group "
+    1.0  F     19.00000 "fluorine"
+    1.0  I    126.90000 "iodine"
+    1.0  H      1.00800 "H bonded to nitrogen atoms"
+    1.0  IM    35.45000 "assumed to be Cl-"
+    1.0  IP    22.99000 "assumed to be Na+"
+    1.0  IB   131.00000 "'big ion w/ waters' for vacuum (Na+, 6H2O)"
+    1.0  N     14.01000 "sp2 nitrogen in amide groups"
+    1.0  O     16.00000 "carbonyl group oxygen"
+    1.0  P     30.97000 "phosphate"
+    1.0  S     32.06000 "sulphur in disulfide linkage"
+    1.0  Cu    63.55000 "copper"
+    1.0  Fe    55.00000 "iron"
+    1.0  Li     6.94000 "lithium"
+    1.0  K     39.10000 "potassium"
+    1.0  Rb    85.47000 "rubidium"
+    1.0  Cs   132.91000 "cesium"
+    ant  Cl    35.450   "same as cl"
+    2.0  Ca    40.08000 "calcium"
+    1.0  Mg    24.30500 "magnesium"
+    ant  Zn    65.4     "Zn2+, taken from parm99.dat (antechamber)"
+
+
+[LennardJones]
+ver:version key:I value:R value:epsilon
+@unit_R=Angstrom
+@unit_epsilon=kcal/mol
+@format=RE
+;
+;
+;  Rev  I      R       epsilon    comment
+;  --- --- ---------- ---------- -------------------------
+   1.0 Ca   1.600000   0.100000 " calcium from parm91.dat"
+   1.0 H    0.600000   0.015700 " !Ferguson base pair geom."
+   1.0 O    1.661200   0.210000 " OPLS"
+   1.0 C    1.908000   0.086000 " OPLS"
+   1.0 N    1.824000   0.170000 " OPLS"
+   1.0 S    2.000000   0.250000 " W. Cornell CH3SH and CH3SCH3 FEP's"
+   1.0 P    2.100000   0.200000 " JCC,7,(1986),230;"
+   1.0 IM   2.470000   0.100000 " Cl- Smith & Dang, JCP 1994,100:5,3757"
+   1.0 IB   5.000000   0.100000 " solvated ion for vacuum approximation"
+   1.0 Li   1.137000   0.018300 " Li+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 IP   1.868000   0.002770 " Na+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 K    2.658000   0.000328 " K+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 Rb   2.956000   0.000170 " Rb+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 Cs   3.395000   0.000081 " Cs+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 I    2.350000   0.400000 " JCC,7,(1986),230;"
+   1.0 F    1.750000   0.061000 " Gough et al. JCC 13,(1992),963."
+   ant Cl   2.47       0.1      " Cl- Smith & Dang, JCP 1994,100:5,3757, taken from parm99.dat (antechamber)"
+   ant Zn   1.10       0.0125   " Zn2+, Merz,PAK, JACS,113,8262,(1991), taken from parm99.dat (antechamber)"
+   ant Mg   0.7926     0.8947   " Mg2+ Aqvist JPC 1990,94,8021.(adapted), taken from parm99.dat (antechamber)"
+;   ant Cl  1.9480  0.2650  "same as cl"
+;   1.0 Mg   1.170000   0.100000 " magnesium from parm91.dat"
+
+
+[ResidueImproperTorsions]
+key:name
+;
+;
+;    res:atom
+;  -------------
+   ALA:N
+   ALA:C
+   GLY:N
+   GLY:C
+   SER:N
+   SER:C
+   THR:N
+   THR:C
+   LEU:N
+   LEU:C
+   ILE:N
+   ILE:C
+   VAL:N
+   VAL:C
+   ASN:N
+   ASN:C
+   ASN:CG
+   ASN:ND2
+   GLN:N
+   GLN:C
+   GLN:CD
+   GLN:NE2
+   ARG:N
+   ARG:C
+   ARG:CZ
+   ARG:NE
+   ARG:NH1
+   ARG:NH2
+   HIS:N
+   HIS:C
+   HIS:ND1
+   HIS:CD2
+   HIS:CE1
+   HIS:CG
+   HIS:N
+   HIS:C
+   HIS:NE2
+   HIS:CD2
+   HIS:CE1
+   HIS:CG
+   HIS:N
+   HIS:C
+   HIS:ND1
+   HIS:NE2
+   HIS:CD2
+   HIS:CE1
+   HIS:CG
+   TRP:N
+   TRP:C
+   TRP:NE1
+   TRP:CZ2
+   TRP:CH2
+   TRP:CZ3
+   TRP:CE3
+   TRP:CD1
+   TRP:CG
+   PHE:N
+   PHE:C
+   PHE:CD2
+   PHE:CE2
+   PHE:CZ
+   PHE:CE1
+   PHE:CD1
+   PHE:CG
+   TYR:N
+   TYR:C
+   TYR:CD2
+   TYR:CE2
+   TYR:CE1
+   TYR:CD1
+   TYR:CG
+   TYR:CZ
+   GLU:N
+   GLU:C
+   GLU:CD
+   ASP:N
+   ASP:C
+   ASP:CG
+   LYS:N
+   LYS:C
+   LYN:N
+   LYN:C
+   PRO:C
+   PRO:N
+   CYS:N
+   CYS:C
+   CYM:N
+   CYM:C
+   CYS-S:N
+   CYS-S:C
+   MET:N
+   MET:C
+   ACE:C
+   NME:N
+   ASH:N
+   ASH:C
+   ASH:CG
+   GLH:N
+   GLH:C
+   GLH:CD
+   ALA-N:C
+   GLY-N:C
+   SER-N:C
+   THR-N:C
+   LEU-N:C
+   ILE-N:C
+   VAL-N:C
+   ASN-N:C
+   ASN-N:CG
+   ASN-N:ND2
+   GLN-N:C
+   GLN-N:CD
+   GLN-N:NE2
+   ARG-N:C
+   ARG-N:CZ
+   ARG-N:NE
+   ARG-N:NH1
+   ARG-N:NH2
+   HIS-N:C
+   HIS-N:ND1
+   HIS-N:CD2
+   HIS-N:CE1
+   HIS-N:CG
+   HIS-N:C
+   HIS-N:NE2
+   HIS-N:CD2
+   HIS-N:CE1
+   HIS-N:CG
+   HIS-N:C
+   HIS-N:ND1
+   HIS-N:NE2
+   HIS-N:CD2
+   HIS-N:CE1
+   HIS-N:CG
+   TRP-N:C
+   TRP-N:NE1
+   TRP-N:CZ2
+   TRP-N:CH2
+   TRP-N:CZ3
+   TRP-N:CE3
+   TRP-N:CD1
+   TRP-N:CG
+   PHE-N:C
+   PHE-N:CD2
+   PHE-N:CE2
+   PHE-N:CZ
+   PHE-N:CE1
+   PHE-N:CD1
+   PHE-N:CG
+   TYR-N:C
+   TYR-N:CD2
+   TYR-N:CE2
+   TYR-N:CE1
+   TYR-N:CD1
+   TYR-N:CG
+   TYR-N:CZ
+   GLU-N:C
+   GLU-N:CD
+   ASP-N:C
+   ASP-N:CG
+   LYS-N:C
+   PRO-N:C
+   CYS-N:C
+   CYS-NS:C
+   MET-N:C
+   ALA-C:N
+   ALA-C:C
+   GLY-C:N
+   GLY-C:C
+   SER-C:N
+   SER-C:C
+   THR-C:N
+   THR-C:C
+   LEU-C:N
+   LEU-C:C
+   ILE-C:N
+   ILE-C:C
+   VAL-C:N
+   VAL-C:C
+   ASN-C:N
+   ASN-C:C
+   ASN-C:CG
+   ASN-C:ND2
+   GLN-C:N
+   GLN-C:C
+   GLN-C:CD
+   GLN-C:NE2
+   ARG-C:N
+   ARG-C:C
+   ARG-C:CZ
+   ARG-C:NE
+   ARG-C:NH1
+   ARG-C:NH2
+   HIS-C:N
+   HIS-C:C
+   HIS-C:ND1
+   HIS-C:CD2
+   HIS-C:CE1
+   HIS-C:CG
+   HIS-C:N
+   HIS-C:C
+   HIS-C:NE2
+   HIS-C:CD2
+   HIS-C:CE1
+   HIS-C:CG
+   HIS-C:N
+   HIS-C:C
+   HIS-C:ND1
+   HIS-C:NE2
+   HIS-C:CD2
+   HIS-C:CE1
+   HIS-C:CG
+   TRP-C:N
+   TRP-C:C
+   TRP-C:NE1
+   TRP-C:CZ2
+   TRP-C:CH2
+   TRP-C:CZ3
+   TRP-C:CE3
+   TRP-C:CD1
+   TRP-C:CG
+   PHE-C:N
+   PHE-C:C
+   PHE-C:CD2
+   PHE-C:CE2
+   PHE-C:CZ
+   PHE-C:CE1
+   PHE-C:CD1
+   PHE-C:CG
+   TYR-C:N
+   TYR-C:C
+   TYR-C:CD2
+   TYR-C:CE2
+   TYR-C:CE1
+   TYR-C:CD1
+   TYR-C:CG
+   TYR-C:CZ
+   GLU-C:N
+   GLU-C:C
+   GLU-C:CD
+   ASP-C:N
+   ASP-C:C
+   ASP-C:CG
+   LYS-C:N
+   LYS-C:C
+   PRO-C:C
+   PRO-C:N
+   CYS-C:N
+   CYS-C:C
+   CYS-CS:N
+   CYS-CS:C
+   MET-C:N
+   MET-C:C
+
+[ChargesAndTypeNames]
+ver:version key:name value:q value:type
+@unit_q=e0
+   1.0 ALA:N      -0.41570 N
+   1.0 ALA:H       0.27190 H
+   1.0 ALA:CA      0.03370 CT
+   1.0 ALA:HA      0.08230 H1
+   1.0 ALA:CB     -0.18250 CT
+   1.0 ALA:1HB     0.06030 HC
+   1.0 ALA:2HB     0.06030 HC
+   1.0 ALA:3HB     0.06030 HC
+   1.0 ALA:C       0.59730 C
+   1.0 ALA:O      -0.56790 O
+   1.0 GLY:N      -0.41570 N
+   1.0 GLY:H       0.27190 H
+   1.0 GLY:CA     -0.02520 CT
+   1.0 GLY:1HA     0.06980 H1
+   1.0 GLY:2HA     0.06980 H1
+   1.0 GLY:C       0.59730 C
+   1.0 GLY:O      -0.56790 O
+   1.0 SER:N      -0.41570 N
+   1.0 SER:H       0.27190 H
+   1.0 SER:CA     -0.02490 CT
+   1.0 SER:HA      0.08430 H1
+   1.0 SER:CB      0.21170 CT
+   1.0 SER:1HB     0.03520 H1
+   1.0 SER:2HB     0.03520 H1
+   1.0 SER:OG     -0.65460 OH
+   1.0 SER:HG      0.42750 HO
+   1.0 SER:C       0.59730 C
+   1.0 SER:O      -0.56790 O
+   1.0 THR:N      -0.41570 N
+   1.0 THR:H       0.27190 H
+   1.0 THR:CA     -0.03890 CT
+   1.0 THR:HA      0.10070 H1
+   1.0 THR:CB      0.36540 CT
+   1.0 THR:HB      0.00430 H1
+   1.0 THR:CG2    -0.24380 CT
+   1.0 THR:1HG2    0.06420 HC
+   1.0 THR:2HG2    0.06420 HC
+   1.0 THR:3HG2    0.06420 HC
+   1.0 THR:OG1    -0.67610 OH
+   1.0 THR:HG1     0.41020 HO
+   1.0 THR:C       0.59730 C
+   1.0 THR:O      -0.56790 O
+   1.0 LEU:N      -0.41570 N
+   1.0 LEU:H       0.27190 H
+   1.0 LEU:CA     -0.05180 CT
+   1.0 LEU:HA      0.09220 H1
+   1.0 LEU:CB     -0.11020 CT
+   1.0 LEU:1HB     0.04570 HC
+   1.0 LEU:2HB     0.04570 HC
+   1.0 LEU:CG      0.35310 CT
+   1.0 LEU:HG     -0.03610 HC
+   1.0 LEU:CD1    -0.41210 CT
+   1.0 LEU:1HD1    0.10000 HC
+   1.0 LEU:2HD1    0.10000 HC
+   1.0 LEU:3HD1    0.10000 HC
+   1.0 LEU:CD2    -0.41210 CT
+   1.0 LEU:1HD2    0.10000 HC
+   1.0 LEU:2HD2    0.10000 HC
+   1.0 LEU:3HD2    0.10000 HC
+   1.0 LEU:C       0.59730 C
+   1.0 LEU:O      -0.56790 O
+   1.0 ILE:N      -0.41570 N
+   1.0 ILE:H       0.27190 H
+   1.0 ILE:CA     -0.05970 CT
+   1.0 ILE:HA      0.08690 H1
+   1.0 ILE:CB      0.13030 CT
+   1.0 ILE:HB      0.01870 HC
+   1.0 ILE:CG2    -0.32040 CT
+   1.0 ILE:1HG2    0.08820 HC
+   1.0 ILE:2HG2    0.08820 HC
+   1.0 ILE:3HG2    0.08820 HC
+   1.0 ILE:CG1    -0.04300 CT
+   1.0 ILE:1HG1    0.02360 HC
+   1.0 ILE:2HG1    0.02360 HC
+   1.0 ILE:CD1    -0.06600 CT
+   1.0 ILE:1HD1    0.01860 HC
+   1.0 ILE:2HD1    0.01860 HC
+   1.0 ILE:3HD1    0.01860 HC
+   1.0 ILE:C       0.59730 C
+   1.0 ILE:O      -0.56790 O
+   1.0 VAL:N      -0.41570 N
+   1.0 VAL:H       0.27190 H
+   1.0 VAL:CA     -0.08750 CT
+   1.0 VAL:HA      0.09690 H1
+   1.0 VAL:CB      0.29850 CT
+   1.0 VAL:HB     -0.02970 HC
+   1.0 VAL:CG1    -0.31920 CT
+   1.0 VAL:1HG1    0.07910 HC
+   1.0 VAL:2HG1    0.07910 HC
+   1.0 VAL:3HG1    0.07910 HC
+   1.0 VAL:CG2    -0.31920 CT
+   1.0 VAL:1HG2    0.07910 HC
+   1.0 VAL:2HG2    0.07910 HC
+   1.0 VAL:3HG2    0.07910 HC
+   1.0 VAL:C       0.59730 C
+   1.0 VAL:O      -0.56790 O
+   1.0 ASN:N      -0.41570 N
+   1.0 ASN:H       0.27190 H
+   1.0 ASN:CA      0.01430 CT
+   1.0 ASN:HA      0.10480 H1
+   1.0 ASN:CB     -0.20410 CT
+   1.0 ASN:1HB     0.07970 HC
+   1.0 ASN:2HB     0.07970 HC
+   1.0 ASN:CG      0.71300 C
+   1.0 ASN:OD1    -0.59310 O
+   1.0 ASN:ND2    -0.91910 N
+   1.0 ASN:1HD2    0.41960 H
+   1.0 ASN:2HD2    0.41960 H
+   1.0 ASN:C       0.59730 C
+   1.0 ASN:O      -0.56790 O
+   1.0 GLN:N      -0.41570 N
+   1.0 GLN:H       0.27190 H
+   1.0 GLN:CA     -0.00310 CT
+   1.0 GLN:HA      0.08500 H1
+   1.0 GLN:CB     -0.00360 CT
+   1.0 GLN:1HB     0.01710 HC
+   1.0 GLN:2HB     0.01710 HC
+   1.0 GLN:CG     -0.06450 CT
+   1.0 GLN:1HG     0.03520 HC
+   1.0 GLN:2HG     0.03520 HC
+   1.0 GLN:CD      0.69510 C
+   1.0 GLN:OE1    -0.60860 O
+   1.0 GLN:NE2    -0.94070 N
+   1.0 GLN:1HE2    0.42510 H
+   1.0 GLN:2HE2    0.42510 H
+   1.0 GLN:C       0.59730 C
+   1.0 GLN:O      -0.56790 O
+   1.0 ARG:N      -0.34790 N
+   1.0 ARG:H       0.27470 H
+   1.0 ARG:CA     -0.26370 CT
+   1.0 ARG:HA      0.15600 H1
+   1.0 ARG:CB     -0.00070 CT
+   1.0 ARG:1HB     0.03270 HC
+   1.0 ARG:2HB     0.03270 HC
+   1.0 ARG:CG      0.03900 CT
+   1.0 ARG:1HG     0.02850 HC
+   1.0 ARG:2HG     0.02850 HC
+   1.0 ARG:CD      0.04860 CT
+   1.0 ARG:1HD     0.06870 H1
+   1.0 ARG:2HD     0.06870 H1
+   1.0 ARG:NE     -0.52950 N2
+   1.0 ARG:HE      0.34560 H
+   1.0 ARG:CZ      0.80760 CA
+   1.0 ARG:NH1    -0.86270 N2
+   1.0 ARG:1HH1    0.44780 H
+   1.0 ARG:2HH1    0.44780 H
+   1.0 ARG:NH2    -0.86270 N2
+   1.0 ARG:1HH2    0.44780 H
+   1.0 ARG:2HH2    0.44780 H
+   1.0 ARG:C       0.73410 C
+   1.0 ARG:O      -0.58940 O
+   1.0 HIS:N      -0.34790 N
+   1.0 HIS:H       0.27470 H
+   1.0 HIS:CA     -0.13540 CT
+   1.0 HIS:HA      0.12120 H1
+   1.0 HIS:CB     -0.04140 CT
+   1.0 HIS:1HB     0.08100 HC
+   1.0 HIS:2HB     0.08100 HC
+   1.0 HIS:CG     -0.00120 CC
+   1.0 HIS:ND1    -0.15130 NA
+   1.0 HIS:HD1     0.38660 H
+   1.0 HIS:CE1    -0.01700 CR
+   1.0 HIS:HE1     0.26810 H5
+   1.0 HIS:NE2    -0.17180 NA
+   1.0 HIS:CD2    -0.11410 CW
+   1.0 HIS:HD2     0.23170 H4
+   1.0 HIS:C       0.73410 C
+   1.0 HIS:O      -0.58940 O
+   1.0 HIS:N      -0.34790 N
+   1.0 HIS:H       0.27470 H
+   1.0 HIS:CA     -0.13540 CT
+   1.0 HIS:HA      0.12120 H1
+   1.0 HIS:CB     -0.04140 CT
+   1.0 HIS:1HB     0.08100 HC
+   1.0 HIS:2HB     0.08100 HC
+   1.0 HIS:CG     -0.00120 CC
+   1.0 HIS:ND1    -0.15130 NA
+   1.0 HIS:CE1    -0.01700 CR
+   1.0 HIS:HE1     0.26810 H5
+   1.0 HIS:NE2    -0.17180 NA
+   1.0 HIS:HE2     0.39110 H
+   1.0 HIS:CD2    -0.11410 CW
+   1.0 HIS:HD2     0.23170 H4
+   1.0 HIS:C       0.73410 C
+   1.0 HIS:O      -0.58940 O
+   1.0 HIS:N      -0.34790 N
+   1.0 HIS:H       0.27470 H
+   1.0 HIS:CA     -0.13540 CT
+   1.0 HIS:HA      0.12120 H1
+   1.0 HIS:CB     -0.04140 CT
+   1.0 HIS:1HB     0.08100 HC
+   1.0 HIS:2HB     0.08100 HC
+   1.0 HIS:CG     -0.00120 CC
+   1.0 HIS:ND1    -0.15130 NA
+   1.0 HIS:HD1     0.38660 H
+   1.0 HIS:CE1    -0.01700 CR
+   1.0 HIS:HE1     0.26810 H5
+   1.0 HIS:NE2    -0.17180 NA
+   1.0 HIS:HE2     0.39110 H
+   1.0 HIS:CD2    -0.11410 CW
+   1.0 HIS:HD2     0.23170 H4
+   1.0 HIS:C       0.73410 C
+   1.0 HIS:O      -0.58940 O
+   1.0 TRP:N      -0.41570 N
+   1.0 TRP:H       0.27190 H
+   1.0 TRP:CA     -0.02750 CT
+   1.0 TRP:HA      0.11230 H1
+   1.0 TRP:CB     -0.00500 CT
+   1.0 TRP:1HB     0.03390 HC
+   1.0 TRP:2HB     0.03390 HC
+   1.0 TRP:CG     -0.14150 C*
+   1.0 TRP:CD1    -0.16380 CW
+   1.0 TRP:HD1     0.20620 H4
+   1.0 TRP:NE1    -0.34180 NA
+   1.0 TRP:HE1     0.34120 H
+   1.0 TRP:CE2     0.13800 CN
+   1.0 TRP:CZ2    -0.26010 CA
+   1.0 TRP:HZ2     0.15720 HA
+   1.0 TRP:CH2    -0.11340 CA
+   1.0 TRP:HH2     0.14170 HA
+   1.0 TRP:CZ3    -0.19720 CA
+   1.0 TRP:HZ3     0.14470 HA
+   1.0 TRP:CE3    -0.23870 CA
+   1.0 TRP:HE3     0.17000 HA
+   1.0 TRP:CD2     0.12430 CB
+   1.0 TRP:C       0.59730 C
+   1.0 TRP:O      -0.56790 O
+   1.0 PHE:N      -0.41570 N
+   1.0 PHE:H       0.27190 H
+   1.0 PHE:CA     -0.00240 CT
+   1.0 PHE:HA      0.09780 H1
+   1.0 PHE:CB     -0.03430 CT
+   1.0 PHE:1HB     0.02950 HC
+   1.0 PHE:2HB     0.02950 HC
+   1.0 PHE:CG      0.01180 CA
+   1.0 PHE:CD1    -0.12560 CA
+   1.0 PHE:HD1     0.13300 HA
+   1.0 PHE:CE1    -0.17040 CA
+   1.0 PHE:HE1     0.14300 HA
+   1.0 PHE:CZ     -0.10720 CA
+   1.0 PHE:HZ      0.12970 HA
+   1.0 PHE:CE2    -0.17040 CA
+   1.0 PHE:HE2     0.14300 HA
+   1.0 PHE:CD2    -0.12560 CA
+   1.0 PHE:HD2     0.13300 HA
+   1.0 PHE:C       0.59730 C
+   1.0 PHE:O      -0.56790 O
+   1.0 TYR:N      -0.41570 N
+   1.0 TYR:H       0.27190 H
+   1.0 TYR:CA     -0.00140 CT
+   1.0 TYR:HA      0.08760 H1
+   1.0 TYR:CB     -0.01520 CT
+   1.0 TYR:1HB     0.02950 HC
+   1.0 TYR:2HB     0.02950 HC
+   1.0 TYR:CG     -0.00110 CA
+   1.0 TYR:CD1    -0.19060 CA
+   1.0 TYR:HD1     0.16990 HA
+   1.0 TYR:CE1    -0.23410 CA
+   1.0 TYR:HE1     0.16560 HA
+   1.0 TYR:CZ      0.32260 C
+   1.0 TYR:OH     -0.55790 OH
+   1.0 TYR:HH      0.39920 HO
+   1.0 TYR:CE2    -0.23410 CA
+   1.0 TYR:HE2     0.16560 HA
+   1.0 TYR:CD2    -0.19060 CA
+   1.0 TYR:HD2     0.16990 HA
+   1.0 TYR:C       0.59730 C
+   1.0 TYR:O      -0.56790 O
+   1.0 GLU:N      -0.51630 N
+   1.0 GLU:H       0.29360 H
+   1.0 GLU:CA      0.03970 CT
+   1.0 GLU:HA      0.11050 H1
+   1.0 GLU:CB      0.05600 CT
+   1.0 GLU:1HB    -0.01730 HC
+   1.0 GLU:2HB    -0.01730 HC
+   1.0 GLU:CG      0.01360 CT
+   1.0 GLU:1HG    -0.04250 HC
+   1.0 GLU:2HG    -0.04250 HC
+   1.0 GLU:CD      0.80540 C
+   1.0 GLU:OE1    -0.81880 O2
+   1.0 GLU:OE2    -0.81880 O2
+   1.0 GLU:C       0.53660 C
+   1.0 GLU:O      -0.58190 O
+   1.0 ASP:N      -0.51630 N
+   1.0 ASP:H       0.29360 H
+   1.0 ASP:CA      0.03810 CT
+   1.0 ASP:HA      0.08800 H1
+   1.0 ASP:CB     -0.03030 CT
+   1.0 ASP:1HB    -0.01220 HC
+   1.0 ASP:2HB    -0.01220 HC
+   1.0 ASP:CG      0.79940 C
+   1.0 ASP:OD1    -0.80140 O2
+   1.0 ASP:OD2    -0.80140 O2
+   1.0 ASP:C       0.53660 C
+   1.0 ASP:O      -0.58190 O
+   1.0 LYS:N      -0.34790 N
+   1.0 LYS:H       0.27470 H
+   1.0 LYS:CA     -0.24000 CT
+   1.0 LYS:HA      0.14260 H1
+   1.0 LYS:CB     -0.00940 CT
+   1.0 LYS:1HB     0.03620 HC
+   1.0 LYS:2HB     0.03620 HC
+   1.0 LYS:CG      0.01870 CT
+   1.0 LYS:1HG     0.01030 HC
+   1.0 LYS:2HG     0.01030 HC
+   1.0 LYS:CD     -0.04790 CT
+   1.0 LYS:1HD     0.06210 HC
+   1.0 LYS:2HD     0.06210 HC
+   1.0 LYS:CE     -0.01430 CT
+   1.0 LYS:1HE     0.11350 HP
+   1.0 LYS:2HE     0.11350 HP
+   1.0 LYS:NZ     -0.38540 N3
+   1.0 LYS:1HZ     0.34000 H
+   1.0 LYS:2HZ     0.34000 H
+   1.0 LYS:3HZ     0.34000 H
+   1.0 LYS:C       0.73410 C
+   1.0 LYS:O      -0.58940 O
+   1.0 LYN:N      -0.41570 N
+   1.0 LYN:H       0.27190 H
+   1.0 LYN:CA     -0.07206 CT
+   1.0 LYN:HA      0.09940 H1
+   1.0 LYN:CB     -0.04845 CT
+   1.0 LYN:HB2     0.03400 HC
+   1.0 LYN:HB3     0.03400 HC
+   1.0 LYN:CG      0.06612 CT
+   1.0 LYN:HG2     0.01041 HC
+   1.0 LYN:HG3     0.01041 HC
+   1.0 LYN:CD     -0.03768 CT
+   1.0 LYN:HD2     0.01155 HC
+   1.0 LYN:HD3     0.01155 HC
+   1.0 LYN:CE      0.32604 CT
+   1.0 LYN:HE2    -0.03358 HP
+   1.0 LYN:HE3    -0.03358 HP
+   1.0 LYN:NZ     -1.03581 N3
+   1.0 LYN:HZ2     0.38604 H
+   1.0 LYN:HZ3     0.38604 H
+   1.0 LYN:C       0.59730 C
+   1.0 LYN:O      -0.56790 O
+   1.0 PRO:N      -0.25480 N
+   1.0 PRO:CD      0.01920 CT
+   1.0 PRO:1HD     0.03910 H1
+   1.0 PRO:2HD     0.03910 H1
+   1.0 PRO:CG      0.01890 CT
+   1.0 PRO:1HG     0.02130 HC
+   1.0 PRO:2HG     0.02130 HC
+   1.0 PRO:CB     -0.00700 CT
+   1.0 PRO:1HB     0.02530 HC
+   1.0 PRO:2HB     0.02530 HC
+   1.0 PRO:CA     -0.02660 CT
+   1.0 PRO:HA      0.06410 H1
+   1.0 PRO:C       0.58960 C
+   1.0 PRO:O      -0.57480 O
+   1.0 CYS:N      -0.41570 N
+   1.0 CYS:H       0.27190 H
+   1.0 CYS:CA      0.02130 CT
+   1.0 CYS:HA      0.11240 H1
+   1.0 CYS:CB     -0.12310 CT
+   1.0 CYS:1HB     0.11120 H1
+   1.0 CYS:2HB     0.11120 H1
+   1.0 CYS:SG     -0.31190 SH
+   1.0 CYS:HG      0.19330 HS
+   1.0 CYS:C       0.59730 C
+   1.0 CYS:O      -0.56790 O
+   1.0 CYM:N      -0.46300 N
+   1.0 CYM:HN      0.25200 H
+   1.0 CYM:CA      0.03500 CT
+   1.0 CYM:HA      0.04800 H1
+   1.0 CYM:CB     -0.73600 CT
+   1.0 CYM:HB3     0.24400 H1
+   1.0 CYM:HB2     0.24400 H1
+   1.0 CYM:SG     -0.73600 SH
+   1.0 CYM:C       0.61600 C
+   1.0 CYM:O      -0.50400 O
+   1.0 CYS-S:N    -0.41570 N
+   1.0 CYS-S:H     0.27190 H
+   1.0 CYS-S:CA    0.04290 CT
+   1.0 CYS-S:HA    0.07660 H1
+   1.0 CYS-S:CB   -0.07900 CT
+   1.0 CYS-S:1HB   0.09100 H1
+   1.0 CYS-S:2HB   0.09100 H1
+   1.0 CYS-S:SG   -0.10810 S
+   1.0 CYS-S:C     0.59730 C
+   1.0 CYS-S:O    -0.56790 O
+   1.0 MET:N      -0.41570 N
+   1.0 MET:H       0.27190 H
+   1.0 MET:CA     -0.02370 CT
+   1.0 MET:HA      0.08800 H1
+   1.0 MET:CB      0.03420 CT
+   1.0 MET:1HB     0.02410 HC
+   1.0 MET:2HB     0.02410 HC
+   1.0 MET:CG      0.00180 CT
+   1.0 MET:1HG     0.04400 H1
+   1.0 MET:2HG     0.04400 H1
+   1.0 MET:SD     -0.27370 S
+   1.0 MET:CE     -0.05360 CT
+   1.0 MET:1HE     0.06840 H1
+   1.0 MET:2HE     0.06840 H1
+   1.0 MET:3HE     0.06840 H1
+   1.0 MET:C       0.59730 C
+   1.0 MET:O      -0.56790 O
+   1.0 ACE:1HH3    0.11230 HC
+   1.0 ACE:CH3    -0.36620 CT
+   1.0 ACE:2HH3    0.11230 HC
+   1.0 ACE:3HH3    0.11230 HC
+   1.0 ACE:C       0.59720 C
+   1.0 ACE:O      -0.56790 O
+   1.0 HOH:1H      0.41700 HW
+   1.0 HOH:O      -0.83400 OW
+   1.0 HOH:2H      0.41700 HW
+   1.0 HOH:H1      0.41700 HW
+   1.0 HOH:O      -0.83400 OW
+   1.0 HOH:H2      0.41700 HW
+   1.0 WAT:1H      0.41700 HW
+   1.0 WAT:O      -0.83400 OW
+   1.0 WAT:2H      0.41700 HW
+   1.0 ASH:N      -0.41570 N
+   1.0 ASH:H       0.27190 H
+   1.0 ASH:CA      0.03410 CT
+   1.0 ASH:HA      0.08640 H1
+   1.0 ASH:CB     -0.03160 CT
+   1.0 ASH:HB2     0.04880 HC
+   1.0 ASH:HB3     0.04880 HC
+   1.0 ASH:CG      0.64620 C
+   1.0 ASH:OD1    -0.55540 O
+   1.0 ASH:OD2    -0.63760 OH
+   1.0 ASH:HD2     0.47470 HO
+   1.0 ASH:C       0.59730 C
+   1.0 ASH:O      -0.56790 O
+   1.0 GLH:N      -0.41570 N
+   1.0 GLH:H       0.27190 H
+   1.0 GLH:CA      0.01450 CT
+   1.0 GLH:HA      0.07790 H1
+   1.0 GLH:CB     -0.00710 CT
+   1.0 GLH:HB2     0.02560 HC
+   1.0 GLH:HB3     0.02560 HC
+   1.0 GLH:CG     -0.01740 CT
+   1.0 GLH:HG2     0.04300 HC
+   1.0 GLH:HG3     0.04300 HC
+   1.0 GLH:CD      0.68010 C
+   1.0 GLH:OE1    -0.58380 O
+   1.0 GLH:OE2    -0.65110 OH
+   1.0 GLH:HE2     0.46410 HO
+   1.0 GLH:C       0.59730 C
+   1.0 GLH:O      -0.56790 O
+   1.0 CIP:NA+     1.00000 IP
+   1.0 CIM:CL-    -1.00000 IM
+   1.0 ALA-N:N     0.14140 N3
+   1.0 ALA-N:1H    0.19970 H
+   1.0 ALA-N:2H    0.19970 H
+   1.0 ALA-N:3H    0.19970 H
+   1.0 ALA-N:CA    0.09620 CT
+   1.0 ALA-N:HA    0.08890 HP
+   1.0 ALA-N:CB   -0.05970 CT
+   1.0 ALA-N:1HB   0.03000 HC
+   1.0 ALA-N:2HB   0.03000 HC
+   1.0 ALA-N:3HB   0.03000 HC
+   1.0 ALA-N:C     0.61630 C
+   1.0 ALA-N:O    -0.57220 O
+   1.0 GLY-N:N     0.29430 N3
+   1.0 GLY-N:1H    0.16420 H
+   1.0 GLY-N:2H    0.16420 H
+   1.0 GLY-N:3H    0.16420 H
+   1.0 GLY-N:CA   -0.01000 CT
+   1.0 GLY-N:1HA   0.08950 HP
+   1.0 GLY-N:2HA   0.08950 HP
+   1.0 GLY-N:C     0.61630 C
+   1.0 GLY-N:O    -0.57220 O
+   1.0 SER-N:N     0.18490 N3
+   1.0 SER-N:1H    0.18980 H
+   1.0 SER-N:2H    0.18980 H
+   1.0 SER-N:3H    0.18980 H
+   1.0 SER-N:CA    0.05670 CT
+   1.0 SER-N:HA    0.07820 HP
+   1.0 SER-N:CB    0.25960 CT
+   1.0 SER-N:1HB   0.02730 H1
+   1.0 SER-N:2HB   0.02730 H1
+   1.0 SER-N:OG   -0.67140 OH
+   1.0 SER-N:HG    0.42390 HO
+   1.0 SER-N:C     0.61630 C
+   1.0 SER-N:O    -0.57220 O
+   1.0 THR-N:N     0.18120 N3
+   1.0 THR-N:1H    0.19340 H
+   1.0 THR-N:2H    0.19340 H
+   1.0 THR-N:3H    0.19340 H
+   1.0 THR-N:CA    0.00340 CT
+   1.0 THR-N:HA    0.10870 HP
+   1.0 THR-N:CB    0.45140 CT
+   1.0 THR-N:HB   -0.03230 H1
+   1.0 THR-N:CG2  -0.25540 CT
+   1.0 THR-N:1HG2  0.06270 HC
+   1.0 THR-N:2HG2  0.06270 HC
+   1.0 THR-N:3HG2  0.06270 HC
+   1.0 THR-N:OG1  -0.67640 OH
+   1.0 THR-N:HG1   0.40700 HO
+   1.0 THR-N:C     0.61630 C
+   1.0 THR-N:O    -0.57220 O
+   1.0 LEU-N:N     0.10100 N3
+   1.0 LEU-N:1H    0.21480 H
+   1.0 LEU-N:2H    0.21480 H
+   1.0 LEU-N:3H    0.21480 H
+   1.0 LEU-N:CA    0.01040 CT
+   1.0 LEU-N:HA    0.10530 HP
+   1.0 LEU-N:CB   -0.02440 CT
+   1.0 LEU-N:1HB   0.02560 HC
+   1.0 LEU-N:2HB   0.02560 HC
+   1.0 LEU-N:CG    0.34210 CT
+   1.0 LEU-N:HG   -0.03800 HC
+   1.0 LEU-N:CD1  -0.41060 CT
+   1.0 LEU-N:1HD1  0.09800 HC
+   1.0 LEU-N:2HD1  0.09800 HC
+   1.0 LEU-N:3HD1  0.09800 HC
+   1.0 LEU-N:CD2  -0.41040 CT
+   1.0 LEU-N:1HD2  0.09800 HC
+   1.0 LEU-N:2HD2  0.09800 HC
+   1.0 LEU-N:3HD2  0.09800 HC
+   1.0 LEU-N:C     0.61230 C
+   1.0 LEU-N:O    -0.57130 O
+   1.0 ILE-N:N     0.03110 N3
+   1.0 ILE-N:1H    0.23290 H
+   1.0 ILE-N:2H    0.23290 H
+   1.0 ILE-N:3H    0.23290 H
+   1.0 ILE-N:CA    0.02570 CT
+   1.0 ILE-N:HA    0.10310 HP
+   1.0 ILE-N:CB    0.18850 CT
+   1.0 ILE-N:HB    0.02130 HC
+   1.0 ILE-N:CG2  -0.37200 CT
+   1.0 ILE-N:1HG2  0.09470 HC
+   1.0 ILE-N:2HG2  0.09470 HC
+   1.0 ILE-N:3HG2  0.09470 HC
+   1.0 ILE-N:CG1  -0.03870 CT
+   1.0 ILE-N:1HG1  0.02010 HC
+   1.0 ILE-N:2HG1  0.02010 HC
+   1.0 ILE-N:CD1  -0.09080 CT
+   1.0 ILE-N:1HD1  0.02260 HC
+   1.0 ILE-N:2HD1  0.02260 HC
+   1.0 ILE-N:3HD1  0.02260 HC
+   1.0 ILE-N:C     0.61230 C
+   1.0 ILE-N:O    -0.57130 O
+   1.0 VAL-N:N     0.05770 N3
+   1.0 VAL-N:1H    0.22720 H
+   1.0 VAL-N:2H    0.22720 H
+   1.0 VAL-N:3H    0.22720 H
+   1.0 VAL-N:CA   -0.00540 CT
+   1.0 VAL-N:HA    0.10930 HP
+   1.0 VAL-N:CB    0.31960 CT
+   1.0 VAL-N:HB   -0.02210 HC
+   1.0 VAL-N:CG1  -0.31290 CT
+   1.0 VAL-N:1HG1  0.07350 HC
+   1.0 VAL-N:2HG1  0.07350 HC
+   1.0 VAL-N:3HG1  0.07350 HC
+   1.0 VAL-N:CG2  -0.31290 CT
+   1.0 VAL-N:1HG2  0.07350 HC
+   1.0 VAL-N:2HG2  0.07350 HC
+   1.0 VAL-N:3HG2  0.07350 HC
+   1.0 VAL-N:C     0.61630 C
+   1.0 VAL-N:O    -0.57220 O
+   1.0 ASN-N:N     0.18010 N3
+   1.0 ASN-N:1H    0.19210 H
+   1.0 ASN-N:2H    0.19210 H
+   1.0 ASN-N:3H    0.19210 H
+   1.0 ASN-N:CA    0.03680 CT
+   1.0 ASN-N:HA    0.12310 HP
+   1.0 ASN-N:CB   -0.02830 CT
+   1.0 ASN-N:1HB   0.05150 HC
+   1.0 ASN-N:2HB   0.05150 HC
+   1.0 ASN-N:CG    0.58330 C
+   1.0 ASN-N:OD1  -0.57440 O
+   1.0 ASN-N:ND2  -0.86340 N
+   1.0 ASN-N:1HD2  0.40970 H
+   1.0 ASN-N:2HD2  0.40970 H
+   1.0 ASN-N:C     0.61630 C
+   1.0 ASN-N:O    -0.57220 O
+   1.0 GLN-N:N     0.14930 N3
+   1.0 GLN-N:1H    0.19960 H
+   1.0 GLN-N:2H    0.19960 H
+   1.0 GLN-N:3H    0.19960 H
+   1.0 GLN-N:CA    0.05360 CT
+   1.0 GLN-N:HA    0.10150 HP
+   1.0 GLN-N:CB    0.06510 CT
+   1.0 GLN-N:1HB   0.00500 HC
+   1.0 GLN-N:2HB   0.00500 HC
+   1.0 GLN-N:CG   -0.09030 CT
+   1.0 GLN-N:1HG   0.03310 HC
+   1.0 GLN-N:2HG   0.03310 HC
+   1.0 GLN-N:CD    0.73540 C
+   1.0 GLN-N:OE1  -0.61330 O
+   1.0 GLN-N:NE2  -1.00310 N
+   1.0 GLN-N:1HE2  0.44290 H
+   1.0 GLN-N:2HE2  0.44290 H
+   1.0 GLN-N:C     0.61230 C
+   1.0 GLN-N:O    -0.57130 O
+   1.0 ARG-N:N     0.13050 N3
+   1.0 ARG-N:1H    0.20830 H
+   1.0 ARG-N:2H    0.20830 H
+   1.0 ARG-N:3H    0.20830 H
+   1.0 ARG-N:CA   -0.02230 CT
+   1.0 ARG-N:HA    0.12420 HP
+   1.0 ARG-N:CB    0.01180 CT
+   1.0 ARG-N:1HB   0.02260 HC
+   1.0 ARG-N:2HB   0.02260 HC
+   1.0 ARG-N:CG    0.02360 CT
+   1.0 ARG-N:1HG   0.03090 HC
+   1.0 ARG-N:2HG   0.03090 HC
+   1.0 ARG-N:CD    0.09350 CT
+   1.0 ARG-N:1HD   0.05270 H1
+   1.0 ARG-N:2HD   0.05270 H1
+   1.0 ARG-N:NE   -0.56500 N2
+   1.0 ARG-N:HE    0.35920 H
+   1.0 ARG-N:CZ    0.82810 CA
+   1.0 ARG-N:NH1  -0.86930 N2
+   1.0 ARG-N:1HH1  0.44940 H
+   1.0 ARG-N:2HH1  0.44940 H
+   1.0 ARG-N:NH2  -0.86930 N2
+   1.0 ARG-N:1HH2  0.44940 H
+   1.0 ARG-N:2HH2  0.44940 H
+   1.0 ARG-N:C     0.72140 C
+   1.0 ARG-N:O    -0.60130 O
+   1.0 HIS-N:N     0.25600 N3
+   1.0 HIS-N:1H    0.17040 H
+   1.0 HIS-N:2H    0.17040 H
+   1.0 HIS-N:3H    0.17040 H
+   1.0 HIS-N:CA    0.05810 CT
+   1.0 HIS-N:HA    0.10470 HP
+   1.0 HIS-N:CB    0.04840 CT
+   1.0 HIS-N:1HB   0.05310 HC
+   1.0 HIS-N:2HB   0.05310 HC
+   1.0 HIS-N:CG   -0.02360 CC
+   1.0 HIS-N:ND1  -0.15100 NA
+   1.0 HIS-N:HD1   0.38210 H
+   1.0 HIS-N:CE1  -0.00110 CR
+   1.0 HIS-N:HE1   0.26450 H5
+   1.0 HIS-N:NE2  -0.17390 NA
+   1.0 HIS-N:CD2  -0.14330 CW
+   1.0 HIS-N:HD2   0.24950 H4
+   1.0 HIS-N:C     0.72140 C
+   1.0 HIS-N:O    -0.60130 O
+   1.0 HIS-N:N     0.25600 N3
+   1.0 HIS-N:1H    0.17040 H
+   1.0 HIS-N:2H    0.17040 H
+   1.0 HIS-N:3H    0.17040 H
+   1.0 HIS-N:CA    0.05810 CT
+   1.0 HIS-N:HA    0.10470 HP
+   1.0 HIS-N:CB    0.04840 CT
+   1.0 HIS-N:1HB   0.05310 HC
+   1.0 HIS-N:2HB   0.05310 HC
+   1.0 HIS-N:CG   -0.02360 CC
+   1.0 HIS-N:ND1  -0.15100 NA
+   1.0 HIS-N:CE1  -0.00110 CR
+   1.0 HIS-N:HE1   0.26450 H5
+   1.0 HIS-N:NE2  -0.17390 NA
+   1.0 HIS-N:HE2   0.39210 H
+   1.0 HIS-N:CD2  -0.14330 CW
+   1.0 HIS-N:HD2   0.24950 H4
+   1.0 HIS-N:C     0.72140 C
+   1.0 HIS-N:O    -0.60130 O
+   1.0 HIS-N:N     0.25600 N3
+   1.0 HIS-N:1H    0.17040 H
+   1.0 HIS-N:2H    0.17040 H
+   1.0 HIS-N:3H    0.17040 H
+   1.0 HIS-N:CA    0.05810 CT
+   1.0 HIS-N:HA    0.10470 HP
+   1.0 HIS-N:CB    0.04840 CT
+   1.0 HIS-N:1HB   0.05310 HC
+   1.0 HIS-N:2HB   0.05310 HC
+   1.0 HIS-N:CG   -0.02360 CC
+   1.0 HIS-N:ND1  -0.15100 NA
+   1.0 HIS-N:HD1   0.38210 H
+   1.0 HIS-N:CE1  -0.00110 CR
+   1.0 HIS-N:HE1   0.26450 H5
+   1.0 HIS-N:NE2  -0.17390 NA
+   1.0 HIS-N:HE2   0.39210 H
+   1.0 HIS-N:CD2  -0.14330 CW
+   1.0 HIS-N:HD2   0.24950 H4
+   1.0 HIS-N:C     0.72140 C
+   1.0 HIS-N:O    -0.60130 O
+   1.0 TRP-N:N     0.19130 N3
+   1.0 TRP-N:1H    0.18880 H
+   1.0 TRP-N:2H    0.18880 H
+   1.0 TRP-N:3H    0.18880 H
+   1.0 TRP-N:CA    0.04210 CT
+   1.0 TRP-N:HA    0.11620 HP
+   1.0 TRP-N:CB    0.05430 CT
+   1.0 TRP-N:1HB   0.02220 HC
+   1.0 TRP-N:2HB   0.02220 HC
+   1.0 TRP-N:CG   -0.16540 C*
+   1.0 TRP-N:CD1  -0.17880 CW
+   1.0 TRP-N:HD1   0.21950 H4
+   1.0 TRP-N:NE1  -0.34440 NA
+   1.0 TRP-N:HE1   0.34120 H
+   1.0 TRP-N:CE2   0.15750 CN
+   1.0 TRP-N:CZ2  -0.27100 CA
+   1.0 TRP-N:HZ2   0.15890 HA
+   1.0 TRP-N:CH2  -0.10800 CA
+   1.0 TRP-N:HH2   0.14110 HA
+   1.0 TRP-N:CZ3  -0.20340 CA
+   1.0 TRP-N:HZ3   0.14580 HA
+   1.0 TRP-N:CE3  -0.22650 CA
+   1.0 TRP-N:HE3   0.16460 HA
+   1.0 TRP-N:CD2   0.11320 CB
+   1.0 TRP-N:C     0.61230 C
+   1.0 TRP-N:O    -0.57130 O
+   1.0 PHE-N:N     0.17370 N3
+   1.0 PHE-N:1H    0.19210 H
+   1.0 PHE-N:2H    0.19210 H
+   1.0 PHE-N:3H    0.19210 H
+   1.0 PHE-N:CA    0.07330 CT
+   1.0 PHE-N:HA    0.10410 HP
+   1.0 PHE-N:CB    0.03300 CT
+   1.0 PHE-N:1HB   0.01040 HC
+   1.0 PHE-N:2HB   0.01040 HC
+   1.0 PHE-N:CG    0.00310 CA
+   1.0 PHE-N:CD1  -0.13920 CA
+   1.0 PHE-N:HD1   0.13740 HA
+   1.0 PHE-N:CE1  -0.16020 CA
+   1.0 PHE-N:HE1   0.14330 HA
+   1.0 PHE-N:CZ   -0.12080 CA
+   1.0 PHE-N:HZ    0.13290 HA
+   1.0 PHE-N:CE2  -0.16030 CA
+   1.0 PHE-N:HE2   0.14330 HA
+   1.0 PHE-N:CD2  -0.13910 CA
+   1.0 PHE-N:HD2   0.13740 HA
+   1.0 PHE-N:C     0.61230 C
+   1.0 PHE-N:O    -0.57130 O
+   1.0 TYR-N:N     0.19400 N3
+   1.0 TYR-N:1H    0.18730 H
+   1.0 TYR-N:2H    0.18730 H
+   1.0 TYR-N:3H    0.18730 H
+   1.0 TYR-N:CA    0.05700 CT
+   1.0 TYR-N:HA    0.09830 HP
+   1.0 TYR-N:CB    0.06590 CT
+   1.0 TYR-N:1HB   0.01020 HC
+   1.0 TYR-N:2HB   0.01020 HC
+   1.0 TYR-N:CG   -0.02050 CA
+   1.0 TYR-N:CD1  -0.20020 CA
+   1.0 TYR-N:HD1   0.17200 HA
+   1.0 TYR-N:CE1  -0.22390 CA
+   1.0 TYR-N:HE1   0.16500 HA
+   1.0 TYR-N:CZ    0.31390 C
+   1.0 TYR-N:OH   -0.55780 OH
+   1.0 TYR-N:HH    0.40010 HO
+   1.0 TYR-N:CE2  -0.22390 CA
+   1.0 TYR-N:HE2   0.16500 HA
+   1.0 TYR-N:CD2  -0.20020 CA
+   1.0 TYR-N:HD2   0.17200 HA
+   1.0 TYR-N:C     0.61230 C
+   1.0 TYR-N:O    -0.57130 O
+   1.0 GLU-N:N     0.00170 N3
+   1.0 GLU-N:1H    0.23910 H
+   1.0 GLU-N:2H    0.23910 H
+   1.0 GLU-N:3H    0.23910 H
+   1.0 GLU-N:CA    0.05880 CT
+   1.0 GLU-N:HA    0.12020 HP
+   1.0 GLU-N:CB    0.09090 CT
+   1.0 GLU-N:1HB  -0.02320 HC
+   1.0 GLU-N:2HB  -0.02320 HC
+   1.0 GLU-N:CG   -0.02360 CT
+   1.0 GLU-N:1HG  -0.03150 HC
+   1.0 GLU-N:2HG  -0.03150 HC
+   1.0 GLU-N:CD    0.80870 C
+   1.0 GLU-N:OE1  -0.81890 O2
+   1.0 GLU-N:OE2  -0.81890 O2
+   1.0 GLU-N:C     0.56210 C
+   1.0 GLU-N:O    -0.58890 O
+   1.0 ASP-N:N     0.07820 N3
+   1.0 ASP-N:1H    0.22000 H
+   1.0 ASP-N:2H    0.22000 H
+   1.0 ASP-N:3H    0.22000 H
+   1.0 ASP-N:CA    0.02920 CT
+   1.0 ASP-N:HA    0.11410 HP
+   1.0 ASP-N:CB   -0.02350 CT
+   1.0 ASP-N:1HB  -0.01690 HC
+   1.0 ASP-N:2HB  -0.01690 HC
+   1.0 ASP-N:CG    0.81940 C
+   1.0 ASP-N:OD1  -0.80840 O2
+   1.0 ASP-N:OD2  -0.80840 O2
+   1.0 ASP-N:C     0.56210 C
+   1.0 ASP-N:O    -0.58890 O
+   1.0 LYS-N:N     0.09660 N3
+   1.0 LYS-N:1H    0.21650 H
+   1.0 LYS-N:2H    0.21650 H
+   1.0 LYS-N:3H    0.21650 H
+   1.0 LYS-N:CA   -0.00150 CT
+   1.0 LYS-N:HA    0.11800 HP
+   1.0 LYS-N:CB    0.02120 CT
+   1.0 LYS-N:1HB   0.02830 HC
+   1.0 LYS-N:2HB   0.02830 HC
+   1.0 LYS-N:CG   -0.00480 CT
+   1.0 LYS-N:1HG   0.01210 HC
+   1.0 LYS-N:2HG   0.01210 HC
+   1.0 LYS-N:CD   -0.06080 CT
+   1.0 LYS-N:1HD   0.06330 HC
+   1.0 LYS-N:2HD   0.06330 HC
+   1.0 LYS-N:CE   -0.01810 CT
+   1.0 LYS-N:1HE   0.11710 HP
+   1.0 LYS-N:2HE   0.11710 HP
+   1.0 LYS-N:NZ   -0.37640 N3
+   1.0 LYS-N:1HZ   0.33820 H
+   1.0 LYS-N:2HZ   0.33820 H
+   1.0 LYS-N:3HZ   0.33820 H
+   1.0 LYS-N:C     0.72140 C
+   1.0 LYS-N:O    -0.60130 O
+   1.0 PRO-N:N    -0.20200 N3
+   1.0 PRO-N:1H    0.31200 H
+   1.0 PRO-N:2H    0.31200 H
+   1.0 PRO-N:3H    0.31200 H
+   1.0 PRO-N:CD   -0.01200 CT
+   1.0 PRO-N:1HD   0.10000 HP
+   1.0 PRO-N:2HD   0.10000 HP
+   1.0 PRO-N:CG   -0.12100 CT
+   1.0 PRO-N:1HG   0.10000 HC
+   1.0 PRO-N:2HG   0.10000 HC
+   1.0 PRO-N:CB   -0.11500 CT
+   1.0 PRO-N:1HB   0.10000 HC
+   1.0 PRO-N:2HB   0.10000 HC
+   1.0 PRO-N:CA    0.10000 CT
+   1.0 PRO-N:HA    0.10000 HP
+   1.0 PRO-N:C     0.52600 C
+   1.0 PRO-N:O    -0.50000 O
+   1.0 CYS-N:N     0.13250 N3
+   1.0 CYS-N:1H    0.20230 H
+   1.0 CYS-N:2H    0.20230 H
+   1.0 CYS-N:3H    0.20230 H
+   1.0 CYS-N:CA    0.09270 CT
+   1.0 CYS-N:HA    0.14110 HP
+   1.0 CYS-N:CB   -0.11950 CT
+   1.0 CYS-N:1HB   0.11880 H1
+   1.0 CYS-N:2HB   0.11880 H1
+   1.0 CYS-N:SG   -0.32980 SH
+   1.0 CYS-N:HSG   0.19750 HS
+   1.0 CYS-N:C     0.61230 C
+   1.0 CYS-N:O    -0.57130 O
+   1.0 CYS-NS:N    0.20690 N3
+   1.0 CYS-NS:1H   0.18150 H
+   1.0 CYS-NS:2H   0.18150 H
+   1.0 CYS-NS:3H   0.18150 H
+   1.0 CYS-NS:CA   0.10550 CT
+   1.0 CYS-NS:HA   0.09220 HP
+   1.0 CYS-NS:CB  -0.02770 CT
+   1.0 CYS-NS:1HB  0.06800 H1
+   1.0 CYS-NS:2HB  0.06800 H1
+   1.0 CYS-NS:SG  -0.09840 S
+   1.0 CYS-NS:C    0.61230 C
+   1.0 CYS-NS:O   -0.57130 O
+   1.0 MET-N:N     0.15920 N3
+   1.0 MET-N:1H    0.19840 H
+   1.0 MET-N:2H    0.19840 H
+   1.0 MET-N:3H    0.19840 H
+   1.0 MET-N:CA    0.02210 CT
+   1.0 MET-N:HA    0.11160 HP
+   1.0 MET-N:CB    0.08650 CT
+   1.0 MET-N:1HB   0.01250 HC
+   1.0 MET-N:2HB   0.01250 HC
+   1.0 MET-N:CG    0.03340 CT
+   1.0 MET-N:1HG   0.02920 H1
+   1.0 MET-N:2HG   0.02920 H1
+   1.0 MET-N:SD   -0.27740 S
+   1.0 MET-N:CE   -0.03410 CT
+   1.0 MET-N:1HE   0.05970 H1
+   1.0 MET-N:2HE   0.05970 H1
+   1.0 MET-N:3HE   0.05970 H1
+   1.0 MET-N:C     0.61230 C
+   1.0 MET-N:O    -0.57130 O
+   1.0 ALA-C:N    -0.38210 N
+   1.0 ALA-C:H     0.26810 H
+   1.0 ALA-C:CA   -0.17470 CT
+   1.0 ALA-C:HA    0.10670 H1
+   1.0 ALA-C:CB   -0.20930 CT
+   1.0 ALA-C:1HB   0.07640 HC
+   1.0 ALA-C:2HB   0.07640 HC
+   1.0 ALA-C:3HB   0.07640 HC
+   1.0 ALA-C:C     0.77310 C
+   1.0 ALA-C:O    -0.80550 O2
+   1.0 ALA-C:OXT  -0.80550 O2
+   1.0 GLY-C:N    -0.38210 N
+   1.0 GLY-C:H     0.26810 H
+   1.0 GLY-C:CA   -0.24930 CT
+   1.0 GLY-C:1HA   0.10560 H1
+   1.0 GLY-C:2HA   0.10560 H1
+   1.0 GLY-C:C     0.72310 C
+   1.0 GLY-C:O    -0.78550 O2
+   1.0 GLY-C:OXT  -0.78550 O2
+   1.0 SER-C:N    -0.38210 N
+   1.0 SER-C:H     0.26810 H
+   1.0 SER-C:CA   -0.27220 CT
+   1.0 SER-C:HA    0.13040 H1
+   1.0 SER-C:CB    0.11230 CT
+   1.0 SER-C:1HB   0.08130 H1
+   1.0 SER-C:2HB   0.08130 H1
+   1.0 SER-C:OG   -0.65140 OH
+   1.0 SER-C:HG    0.44740 HO
+   1.0 SER-C:C     0.81130 C
+   1.0 SER-C:O    -0.81320 O2
+   1.0 SER-C:OXT  -0.81320 O2
+   1.0 THR-C:N    -0.38210 N
+   1.0 THR-C:H     0.26810 H
+   1.0 THR-C:CA   -0.24200 CT
+   1.0 THR-C:HA    0.12070 H1
+   1.0 THR-C:CB    0.30250 CT
+   1.0 THR-C:HB    0.00780 H1
+   1.0 THR-C:CG2  -0.18530 CT
+   1.0 THR-C:1HG2  0.05860 HC
+   1.0 THR-C:2HG2  0.05860 HC
+   1.0 THR-C:3HG2  0.05860 HC
+   1.0 THR-C:OG1  -0.64960 OH
+   1.0 THR-C:HG1   0.41190 HO
+   1.0 THR-C:C     0.78100 C
+   1.0 THR-C:O    -0.80440 O2
+   1.0 THR-C:OXT  -0.80440 O2
+   1.0 LEU-C:N    -0.38210 N
+   1.0 LEU-C:H     0.26810 H
+   1.0 LEU-C:CA   -0.28470 CT
+   1.0 LEU-C:HA    0.13460 H1
+   1.0 LEU-C:CB   -0.24690 CT
+   1.0 LEU-C:1HB   0.09740 HC
+   1.0 LEU-C:2HB   0.09740 HC
+   1.0 LEU-C:CG    0.37060 CT
+   1.0 LEU-C:HG   -0.03740 HC
+   1.0 LEU-C:CD1  -0.41630 CT
+   1.0 LEU-C:1HD1  0.10380 HC
+   1.0 LEU-C:2HD1  0.10380 HC
+   1.0 LEU-C:3HD1  0.10380 HC
+   1.0 LEU-C:CD2  -0.41630 CT
+   1.0 LEU-C:1HD2  0.10380 HC
+   1.0 LEU-C:2HD2  0.10380 HC
+   1.0 LEU-C:3HD2  0.10380 HC
+   1.0 LEU-C:C     0.83260 C
+   1.0 LEU-C:O    -0.81990 O2
+   1.0 LEU-C:OXT  -0.81990 O2
+   1.0 ILE-C:N    -0.38210 N
+   1.0 ILE-C:H     0.26810 H
+   1.0 ILE-C:CA   -0.31000 CT
+   1.0 ILE-C:HA    0.13750 H1
+   1.0 ILE-C:CB    0.03630 CT
+   1.0 ILE-C:HB    0.07660 HC
+   1.0 ILE-C:CG2  -0.34980 CT
+   1.0 ILE-C:1HG2  0.10210 HC
+   1.0 ILE-C:2HG2  0.10210 HC
+   1.0 ILE-C:3HG2  0.10210 HC
+   1.0 ILE-C:CG1  -0.03230 CT
+   1.0 ILE-C:1HG1  0.03210 HC
+   1.0 ILE-C:2HG1  0.03210 HC
+   1.0 ILE-C:CD1  -0.06990 CT
+   1.0 ILE-C:1HD1  0.01960 HC
+   1.0 ILE-C:2HD1  0.01960 HC
+   1.0 ILE-C:3HD1  0.01960 HC
+   1.0 ILE-C:C     0.83430 C
+   1.0 ILE-C:O    -0.81900 O2
+   1.0 ILE-C:OXT  -0.81900 O2
+   1.0 NME-C:N      -0.41570 N
+   1.0 NME-C:H       0.27190 H
+   1.0 NME-C:CH3    -0.14900 CT
+   1.0 NME-C:1HH3    0.09760 H1
+   1.0 NME-C:2HH3    0.09760 H1
+   1.0 NME-C:3HH3    0.09760 H1
+   1.0 VAL-C:N    -0.38210 N
+   1.0 VAL-C:H     0.26810 H
+   1.0 VAL-C:CA   -0.34380 CT
+   1.0 VAL-C:HA    0.14380 H1
+   1.0 VAL-C:CB    0.19400 CT
+   1.0 VAL-C:HB    0.03080 HC
+   1.0 VAL-C:CG1  -0.30640 CT
+   1.0 VAL-C:1HG1  0.08360 HC
+   1.0 VAL-C:2HG1  0.08360 HC
+   1.0 VAL-C:3HG1  0.08360 HC
+   1.0 VAL-C:CG2  -0.30640 CT
+   1.0 VAL-C:1HG2  0.08360 HC
+   1.0 VAL-C:2HG2  0.08360 HC
+   1.0 VAL-C:3HG2  0.08360 HC
+   1.0 VAL-C:C     0.83500 C
+   1.0 VAL-C:O    -0.81730 O2
+   1.0 VAL-C:OXT  -0.81730 O2
+   1.0 ASN-C:N    -0.38210 N
+   1.0 ASN-C:H     0.26810 H
+   1.0 ASN-C:CA   -0.20800 CT
+   1.0 ASN-C:HA    0.13580 H1
+   1.0 ASN-C:CB   -0.22990 CT
+   1.0 ASN-C:1HB   0.10230 HC
+   1.0 ASN-C:2HB   0.10230 HC
+   1.0 ASN-C:CG    0.71530 C
+   1.0 ASN-C:OD1  -0.60100 O
+   1.0 ASN-C:ND2  -0.90840 N
+   1.0 ASN-C:1HD2  0.41500 H
+   1.0 ASN-C:2HD2  0.41500 H
+   1.0 ASN-C:C     0.80500 C
+   1.0 ASN-C:O    -0.81470 O2
+   1.0 ASN-C:OXT  -0.81470 O2
+   1.0 GLN-C:N    -0.38210 N
+   1.0 GLN-C:H     0.26810 H
+   1.0 GLN-C:CA   -0.22480 CT
+   1.0 GLN-C:HA    0.12320 H1
+   1.0 GLN-C:CB   -0.06640 CT
+   1.0 GLN-C:1HB   0.04520 HC
+   1.0 GLN-C:2HB   0.04520 HC
+   1.0 GLN-C:CG   -0.02100 CT
+   1.0 GLN-C:1HG   0.02030 HC
+   1.0 GLN-C:2HG   0.02030 HC
+   1.0 GLN-C:CD    0.70930 C
+   1.0 GLN-C:OE1  -0.60980 O
+   1.0 GLN-C:NE2  -0.95740 N
+   1.0 GLN-C:1HE2  0.43040 H
+   1.0 GLN-C:2HE2  0.43040 H
+   1.0 GLN-C:C     0.77750 C
+   1.0 GLN-C:O    -0.80420 O2
+   1.0 GLN-C:OXT  -0.80420 O2
+   1.0 ARG-C:N    -0.34810 N
+   1.0 ARG-C:H     0.27640 H
+   1.0 ARG-C:CA   -0.30680 CT
+   1.0 ARG-C:HA    0.14470 H1
+   1.0 ARG-C:CB   -0.03740 CT
+   1.0 ARG-C:1HB   0.03710 HC
+   1.0 ARG-C:2HB   0.03710 HC
+   1.0 ARG-C:CG    0.07440 CT
+   1.0 ARG-C:1HG   0.01850 HC
+   1.0 ARG-C:2HG   0.01850 HC
+   1.0 ARG-C:CD    0.11140 CT
+   1.0 ARG-C:1HD   0.04680 H1
+   1.0 ARG-C:2HD   0.04680 H1
+   1.0 ARG-C:NE   -0.55640 N2
+   1.0 ARG-C:HE    0.34790 H
+   1.0 ARG-C:CZ    0.83680 CA
+   1.0 ARG-C:NH1  -0.87370 N2
+   1.0 ARG-C:1HH1  0.44930 H
+   1.0 ARG-C:2HH1  0.44930 H
+   1.0 ARG-C:NH2  -0.87370 N2
+   1.0 ARG-C:1HH2  0.44930 H
+   1.0 ARG-C:2HH2  0.44930 H
+   1.0 ARG-C:C     0.85570 C
+   1.0 ARG-C:O    -0.82660 O2
+   1.0 ARG-C:OXT  -0.82660 O2
+   1.0 HIS-C:N    -0.34810 N
+   1.0 HIS-C:H     0.27640 H
+   1.0 HIS-C:CA   -0.14450 CT
+   1.0 HIS-C:HA    0.11150 H1
+   1.0 HIS-C:CB   -0.08000 CT
+   1.0 HIS-C:1HB   0.08680 HC
+   1.0 HIS-C:2HB   0.08680 HC
+   1.0 HIS-C:CG    0.02980 CC
+   1.0 HIS-C:ND1  -0.15010 NA
+   1.0 HIS-C:HD1   0.38830 H
+   1.0 HIS-C:CE1  -0.02510 CR
+   1.0 HIS-C:HE1   0.26940 H5
+   1.0 HIS-C:NE2  -0.16830 NA
+   1.0 HIS-C:CD2  -0.12560 CW
+   1.0 HIS-C:HD2   0.23360 H4
+   1.0 HIS-C:C     0.80320 C
+   1.0 HIS-C:O    -0.81770 O2
+   1.0 HIS-C:OXT  -0.81770 O2
+   1.0 HIS-C:N    -0.34810 N
+   1.0 HIS-C:H     0.27640 H
+   1.0 HIS-C:CA   -0.14450 CT
+   1.0 HIS-C:HA    0.11150 H1
+   1.0 HIS-C:CB   -0.08000 CT
+   1.0 HIS-C:1HB   0.08680 HC
+   1.0 HIS-C:2HB   0.08680 HC
+   1.0 HIS-C:CG    0.02980 CC
+   1.0 HIS-C:ND1  -0.15010 NA
+   1.0 HIS-C:CE1  -0.02510 CR
+   1.0 HIS-C:HE1   0.26940 H5
+   1.0 HIS-C:NE2  -0.16830 NA
+   1.0 HIS-C:HE2   0.39130 H
+   1.0 HIS-C:CD2  -0.12560 CW
+   1.0 HIS-C:HD2   0.23360 H4
+   1.0 HIS-C:C     0.80320 C
+   1.0 HIS-C:O    -0.81770 O2
+   1.0 HIS-C:OXT  -0.81770 O2
+   1.0 HIS-C:N    -0.34810 N
+   1.0 HIS-C:H     0.27640 H
+   1.0 HIS-C:CA   -0.14450 CT
+   1.0 HIS-C:HA    0.11150 H1
+   1.0 HIS-C:CB   -0.08000 CT
+   1.0 HIS-C:1HB   0.08680 HC
+   1.0 HIS-C:2HB   0.08680 HC
+   1.0 HIS-C:CG    0.02980 CC
+   1.0 HIS-C:ND1  -0.15010 NA
+   1.0 HIS-C:HD1   0.38830 H
+   1.0 HIS-C:CE1  -0.02510 CR
+   1.0 HIS-C:HE1   0.26940 H5
+   1.0 HIS-C:NE2  -0.16830 NA
+   1.0 HIS-C:HE2   0.39130 H
+   1.0 HIS-C:CD2  -0.12560 CW
+   1.0 HIS-C:HD2   0.23360 H4
+   1.0 HIS-C:C     0.80320 C
+   1.0 HIS-C:O    -0.81770 O2
+   1.0 HIS-C:OXT  -0.81770 O2
+   1.0 TRP-C:N    -0.38210 N
+   1.0 TRP-C:H     0.26810 H
+   1.0 TRP-C:CA   -0.20840 CT
+   1.0 TRP-C:HA    0.12720 H1
+   1.0 TRP-C:CB   -0.07420 CT
+   1.0 TRP-C:1HB   0.04970 HC
+   1.0 TRP-C:2HB   0.04970 HC
+   1.0 TRP-C:CG   -0.07960 C*
+   1.0 TRP-C:CD1  -0.18080 CW
+   1.0 TRP-C:HD1   0.20430 H4
+   1.0 TRP-C:NE1  -0.33160 NA
+   1.0 TRP-C:HE1   0.34130 H
+   1.0 TRP-C:CE2   0.12220 CN
+   1.0 TRP-C:CZ2  -0.25940 CA
+   1.0 TRP-C:HZ2   0.15670 HA
+   1.0 TRP-C:CH2  -0.10200 CA
+   1.0 TRP-C:HH2   0.14010 HA
+   1.0 TRP-C:CZ3  -0.22870 CA
+   1.0 TRP-C:HZ3   0.15070 HA
+   1.0 TRP-C:CE3  -0.18370 CA
+   1.0 TRP-C:HE3   0.14910 HA
+   1.0 TRP-C:CD2   0.10780 CB
+   1.0 TRP-C:C     0.76580 C
+   1.0 TRP-C:O    -0.80110 O2
+   1.0 TRP-C:OXT  -0.80110 O2
+   1.0 PHE-C:N    -0.38210 N
+   1.0 PHE-C:H     0.26810 H
+   1.0 PHE-C:CA   -0.18250 CT
+   1.0 PHE-C:HA    0.10980 H1
+   1.0 PHE-C:CB   -0.09590 CT
+   1.0 PHE-C:1HB   0.04430 HC
+   1.0 PHE-C:2HB   0.04430 HC
+   1.0 PHE-C:CG    0.05520 CA
+   1.0 PHE-C:CD1  -0.13000 CA
+   1.0 PHE-C:HD1   0.14080 HA
+   1.0 PHE-C:CE1  -0.18470 CA
+   1.0 PHE-C:HE1   0.14610 HA
+   1.0 PHE-C:CZ   -0.09440 CA
+   1.0 PHE-C:HZ    0.12800 HA
+   1.0 PHE-C:CE2  -0.18470 CA
+   1.0 PHE-C:HE2   0.14610 HA
+   1.0 PHE-C:CD2  -0.13000 CA
+   1.0 PHE-C:HD2   0.14080 HA
+   1.0 PHE-C:C     0.76600 C
+   1.0 PHE-C:O    -0.80260 O2
+   1.0 PHE-C:OXT  -0.80260 O2
+   1.0 TYR-C:N    -0.38210 N
+   1.0 TYR-C:H     0.26810 H
+   1.0 TYR-C:CA   -0.20150 CT
+   1.0 TYR-C:HA    0.10920 H1
+   1.0 TYR-C:CB   -0.07520 CT
+   1.0 TYR-C:1HB   0.04900 HC
+   1.0 TYR-C:2HB   0.04900 HC
+   1.0 TYR-C:CG    0.02430 CA
+   1.0 TYR-C:CD1  -0.19220 CA
+   1.0 TYR-C:HD1   0.17800 HA
+   1.0 TYR-C:CE1  -0.24580 CA
+   1.0 TYR-C:HE1   0.16730 HA
+   1.0 TYR-C:CZ    0.33950 C
+   1.0 TYR-C:OH   -0.56430 OH
+   1.0 TYR-C:HH    0.40170 HO
+   1.0 TYR-C:CE2  -0.24580 CA
+   1.0 TYR-C:HE2   0.16730 HA
+   1.0 TYR-C:CD2  -0.19220 CA
+   1.0 TYR-C:HD2   0.17800 HA
+   1.0 TYR-C:C     0.78170 C
+   1.0 TYR-C:O    -0.80700 O2
+   1.0 TYR-C:OXT  -0.80700 O2
+   1.0 GLU-C:N    -0.51920 N
+   1.0 GLU-C:H     0.30550 H
+   1.0 GLU-C:CA   -0.20590 CT
+   1.0 GLU-C:HA    0.13990 H1
+   1.0 GLU-C:CB    0.00710 CT
+   1.0 GLU-C:1HB  -0.00780 HC
+   1.0 GLU-C:2HB  -0.00780 HC
+   1.0 GLU-C:CG    0.06750 CT
+   1.0 GLU-C:1HG  -0.05480 HC
+   1.0 GLU-C:2HG  -0.05480 HC
+   1.0 GLU-C:CD    0.81830 C
+   1.0 GLU-C:OE1  -0.82200 O2
+   1.0 GLU-C:OE2  -0.82200 O2
+   1.0 GLU-C:C     0.74200 C
+   1.0 GLU-C:O    -0.79300 O2
+   1.0 GLU-C:OXT  -0.79300 O2
+   1.0 ASP-C:N    -0.51920 N
+   1.0 ASP-C:H     0.30550 H
+   1.0 ASP-C:CA   -0.18170 CT
+   1.0 ASP-C:HA    0.10460 H1
+   1.0 ASP-C:CB   -0.06770 CT
+   1.0 ASP-C:1HB  -0.02120 HC
+   1.0 ASP-C:2HB  -0.02120 HC
+   1.0 ASP-C:CG    0.88510 C
+   1.0 ASP-C:OD1  -0.81620 O2
+   1.0 ASP-C:OD2  -0.81620 O2
+   1.0 ASP-C:C     0.72560 C
+   1.0 ASP-C:O    -0.78870 O2
+   1.0 ASP-C:OXT  -0.78870 O2
+   1.0 LYS-C:N    -0.34810 N
+   1.0 LYS-C:H     0.27640 H
+   1.0 LYS-C:CA   -0.29030 CT
+   1.0 LYS-C:HA    0.14380 H1
+   1.0 LYS-C:CB   -0.05380 CT
+   1.0 LYS-C:1HB   0.04820 HC
+   1.0 LYS-C:2HB   0.04820 HC
+   1.0 LYS-C:CG    0.02270 CT
+   1.0 LYS-C:1HG   0.01340 HC
+   1.0 LYS-C:2HG   0.01340 HC
+   1.0 LYS-C:CD   -0.03920 CT
+   1.0 LYS-C:1HD   0.06110 HC
+   1.0 LYS-C:2HD   0.06110 HC
+   1.0 LYS-C:CE   -0.01760 CT
+   1.0 LYS-C:1HE   0.11210 HP
+   1.0 LYS-C:2HE   0.11210 HP
+   1.0 LYS-C:NZ   -0.37410 N3
+   1.0 LYS-C:1HZ   0.33740 H
+   1.0 LYS-C:2HZ   0.33740 H
+   1.0 LYS-C:3HZ   0.33740 H
+   1.0 LYS-C:C     0.84880 C
+   1.0 LYS-C:O    -0.82520 O2
+   1.0 LYS-C:OXT  -0.82520 O2
+   1.0 PRO-C:N    -0.28020 N
+   1.0 PRO-C:CD    0.04340 CT
+   1.0 PRO-C:1HD   0.03310 H1
+   1.0 PRO-C:2HD   0.03310 H1
+   1.0 PRO-C:CG    0.04660 CT
+   1.0 PRO-C:1HG   0.01720 HC
+   1.0 PRO-C:2HG   0.01720 HC
+   1.0 PRO-C:CB   -0.05430 CT
+   1.0 PRO-C:1HB   0.03810 HC
+   1.0 PRO-C:2HB   0.03810 HC
+   1.0 PRO-C:CA   -0.13360 CT
+   1.0 PRO-C:HA    0.07760 H1
+   1.0 PRO-C:C     0.66310 C
+   1.0 PRO-C:O    -0.76970 O2
+   1.0 PRO-C:OXT  -0.76970 O2
+   1.0 CYS-C:N    -0.38210 N
+   1.0 CYS-C:H     0.26810 H
+   1.0 CYS-C:CA   -0.16350 CT
+   1.0 CYS-C:HA    0.13960 H1
+   1.0 CYS-C:CB   -0.19960 CT
+   1.0 CYS-C:1HB   0.14370 H1
+   1.0 CYS-C:2HB   0.14370 H1
+   1.0 CYS-C:SG   -0.31020 SH
+   1.0 CYS-C:HSG   0.20680 HS
+   1.0 CYS-C:C     0.74970 C
+   1.0 CYS-C:O    -0.79810 O2
+   1.0 CYS-C:OXT  -0.79810 O2
+   1.0 CYS-CS:N   -0.38210 N
+   1.0 CYS-CS:H    0.26810 H
+   1.0 CYS-CS:CA  -0.13180 CT
+   1.0 CYS-CS:HA   0.09380 H1
+   1.0 CYS-CS:CB  -0.19430 CT
+   1.0 CYS-CS:1HB  0.12280 H1
+   1.0 CYS-CS:2HB  0.12280 H1
+   1.0 CYS-CS:SG  -0.05290 S
+   1.0 CYS-CS:C    0.76180 C
+   1.0 CYS-CS:O   -0.80410 O2
+   1.0 CYS-CS:OXT -0.80410 O2
+   1.0 MET-C:N    -0.38210 N
+   1.0 MET-C:H     0.26810 H
+   1.0 MET-C:CA   -0.25970 CT
+   1.0 MET-C:HA    0.12770 H1
+   1.0 MET-C:CB   -0.02360 CT
+   1.0 MET-C:1HB   0.04800 HC
+   1.0 MET-C:2HB   0.04800 HC
+   1.0 MET-C:CG    0.04920 CT
+   1.0 MET-C:1HG   0.03170 H1
+   1.0 MET-C:2HG   0.03170 H1
+   1.0 MET-C:SD   -0.26920 S
+   1.0 MET-C:CE   -0.03760 CT
+   1.0 MET-C:1HE   0.06250 H1
+   1.0 MET-C:2HE   0.06250 H1
+   1.0 MET-C:3HE   0.06250 H1
+   1.0 MET-C:C     0.80130 C
+   1.0 MET-C:O    -0.81050 O2
+   1.0 MET-C:OXT  -0.81050 O2
+   1.0 CA:CA       2.00000 C0
+   1.0 MG:MG       2.00000 MG
+   1.0 CH4-M:C       0.00000 CT
+   1.0 CH4-M:1H      0.00000 H1
+   1.0 CH4-M:2H      0.00000 H1
+   1.0 CH4-M:3H      0.00000 H1
+   1.0 CH4-M:4H      0.00000 H1
+   1.0 PCA:N      -0.720984 N
+   1.0 PCA:H       0.374677 H
+   1.0 PCA:CA     -0.025874 CT
+   1.0 PCA:C       0.865161 C
+   1.0 PCA:O      -0.798202 O
+   1.0 PCA:CB      0.114954 CT
+   1.0 PCA:CG     -0.126748 CT
+   1.0 PCA:CD      0.770356 C
+   1.0 PCA:OE     -0.682912 O
+   1.0 PCA:HA      0.039708 H1
+   1.0 PCA:1HB     0.000266 HC
+   1.0 PCA:2HB    -0.031861 HC
+   1.0 PCA:1HG     0.034072 HC
+   1.0 PCA:2HG     0.025655 HC
+   1.0 PCA:OXT    -0.838268 O
+   1.0 PCA-N:N      -0.720984 N
+   1.0 PCA-N:H       0.374677 H
+   1.0 PCA-N:CA     -0.025874 CT
+   1.0 PCA-N:C       0.865161 C
+   1.0 PCA-N:O      -0.798202 O
+   1.0 PCA-N:CB      0.114954 CT
+   1.0 PCA-N:CG     -0.126748 CT
+   1.0 PCA-N:CD      0.770356 C
+   1.0 PCA-N:OE     -0.682912 O
+   1.0 PCA-N:HA      0.039708 H1
+   1.0 PCA-N:1HB     0.000266 HC
+   1.0 PCA-N:2HB    -0.031861 HC
+   1.0 PCA-N:1HG     0.034072 HC
+   1.0 PCA-N:2HG     0.025655 HC
+   1.0 PCA-M:N      -0.720984 N
+   1.0 PCA-M:H       0.374677 H
+   1.0 PCA-M:CA     -0.025874 CT
+   1.0 PCA-M:C       0.865161 C
+   1.0 PCA-M:O      -0.798202 O
+   1.0 PCA-M:CB      0.114954 CT
+   1.0 PCA-M:CG     -0.126748 CT
+   1.0 PCA-M:CD      0.770356 C
+   1.0 PCA-M:OE     -0.682912 O
+   1.0 PCA-M:HA      0.039708 H1
+   1.0 PCA-M:1HB     0.000266 HC
+   1.0 PCA-M:2HB    -0.031861 HC
+   1.0 PCA-M:1HG     0.034072 HC
+   1.0 PCA-M:2HG     0.025655 HC
+   1.0 PCA-M:OXT    -0.838268 O
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/atomic_electron_affinities.data	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,88 @@
+# atomic electron affinities, taken from CRC Handbook of Chemistry and Physics, 79th edition, 1998; non-excistant values like unstable ions have 0.0
+0.754593
+0.0
+0.6180
+0.0
+0.277
+1.2629
+0.0
+1.4611103
+3.401190
+0.0
+0.547926
+0.0
+0.441
+1.385
+0.7465
+2.077104
+3.61269
+0.0
+0.50147
+0.02455
+0.188
+0.079
+0.525
+0.666
+0.0
+0.151
+0.662
+1.156
+1.235
+0.0
+0.3
+1.233
+0.81
+2.020670
+3.363590
+0.0
+0.48592
+0.048
+0.307
+0.426
+0.893
+0.748
+0.55
+1.05
+1.137
+0.562
+1.302
+0.0
+0.3
+1.112
+1.046
+1.9708
+3.059038
+0.0
+0.471626
+0.15
+0.5
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.322
+0.815
+0.15
+1.1
+1.5638
+2.128
+2.30863
+0.0
+0.2
+0.364
+0.946
+1.9
+2.8
+0.0
+0.46
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/atomic_ionization_potentials.data	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,73 @@
+# atomic ionization potentials (neutral atom and +1 ion), CRC Handbook of Chemistry and Physics, 79th edition, 1998
+13.59844 20.02
+24.58741 54.41778
+5.39172 75.64018
+9.3227 18.21116
+8.29803 25.15484
+11.26030 24.38332
+14.53414 29.6013
+13.61806 35.11730
+17.42282 34.97082
+21.5646 40.96328
+5.13908 47.2864
+7.64624 15.03528
+5.98577 18.82856
+8.15169 16.34585
+10.48669 19.7694
+10.36001 23.3379
+12.96764 23.814
+15.75962 27.62967
+4.34066 31.63
+6.11316 11.87172
+6.5615 12.79967
+6.8281 13.5755
+6.7463 14.66
+6.7665 16.4857
+7.43402 15.63999
+7.9024 16.1878
+7.8810 17.083
+7.6398 18.16884
+7.72638 20.29240
+9.3942 17.96440
+5.99930 20.5142
+7.8994 15.93462
+9.7886 18.633
+9.75238 21.19
+11.81381 21.8
+13.99961 24.35985
+4.17713 27.285
+5.6949 11.03013
+6.2171 12.24
+6.63390 13.13
+6.75885 14.32
+7.09243 16.16
+7.28 15.26
+7.36050 16.76
+7.45890 18.08
+8.3369 19.43
+7.5763 21.49
+8.9938 16.90832
+5.78636 18.8698
+7.3439 14.63225
+8.6084 16.53051
+9.0096 18.6
+10.45126 19.1313
+12.1298 21.20979
+3.89390 23.15745
+5.21170 10.00390
+5.770 11.060
+5.5387 10.85
+5.464 10.55
+5.5250 10.73
+5.58 10.9
+5.6436 11.07
+5.6704 11.241
+6.1501 12.09
+5.8638 11.52
+5.9389 11.67
+6.0215 11.80
+6.1077 11.93
+6.18431 12.05
+6.25416 12.1761
+5.4259 13.9
+6.82507 14.9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/atomic_polarizabilities.data	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,101 @@
+# atomic ground state polarizabilities, taken from CRC Handbook of Chemistry and Physics, 79th edition, 1998
+0.666793
+0.204956
+24.3
+5.6
+3.03
+1.76
+1.1
+0.802
+0.557
+0.3956
+24.08
+10.6
+6.8
+5.38
+3.63
+2.9
+2.18
+1.6411
+43.4
+22.8
+17.8
+14.6
+12.4
+11.6
+9.4
+8.4
+7.5
+6.8
+6.1
+7.1
+8.12
+6.07
+4.31
+3.77
+3.05
+2.4844
+47.3
+27.6
+22.7
+17.9
+15.7
+12.8
+11.4
+9.6
+8.6
+4.8
+7.2
+7.2
+10.2
+7.7
+6.6
+5.5
+5.35
+4.044
+59.6
+39.7
+31.1
+29.6
+28.2
+31.4
+30.1
+28.8
+27.7
+23.5
+25.5
+24.5
+23.6
+22.7
+21.8
+21.0
+21.9
+16.2
+13.1
+11.1
+9.7
+8.5
+7.6
+6.5
+5.8
+5.7
+7.6
+6.8
+7.4
+6.8
+6.0
+5.3
+48.7
+38.3
+32.1
+32.1
+25.4
+24.9
+24.8
+24.5
+23.3
+23.0
+22.7
+20.5
+19.7
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/dragon_descriptors.txt	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,1665 @@
+MW	molecular weight
+AMW	average molecular weight
+Sv	sum of atomic van der Waals volumes (scaled on Carbon atom)
+Se	sum of atomic Sanderson electronegativities (scaled on Carbon atom)
+Sp	sum of atomic polarizabilities (scaled on Carbon atom)
+Ss	sum of Kier-Hall electrotopological states
+Mv	mean atomic van der Waals volume (scaled on Carbon atom)
+Me	mean atomic Sanderson electronegativity (scaled on Carbon atom)
+Mp	mean atomic polarizability (scaled on Carbon atom)
+Ms	mean electrotopological state
+nAT	number of atoms
+nSK	number of non-H atoms
+nBT	number of bonds
+nBO	number of non-H bonds
+nBM	number of multiple bonds
+SCBO	sum of conventional bond orders (H-depleted)
+ARR	aromatic ratio
+nCIC	number of rings
+nCIR	number of circuits
+RBN	number of rotatable bonds
+RBF	rotatable bond fraction
+nDB	number of double bonds
+nTB	number of triple bonds
+nAB	number of aromatic bonds
+nH	number of Hydrogen atoms
+nC	number of Carbon atoms
+nN	number of Nitrogen atoms
+nO	number of Oxygen atoms
+nP	number of Phosphorous atoms
+nS	number of Sulfur atoms
+nF	number of Fluorine atoms
+nCL	number of Chlorine atoms
+nBR	number of Bromine atoms
+nI	number of Iodine atoms
+nB	number of Boron atoms
+nHM	number of heavy atoms
+nX	number of halogen atoms
+nR03	number of 3-membered rings
+nR04	number of 4-membered rings
+nR05	number of 5-membered rings
+nR06	number of 6-membered rings
+nR07	number of 7-membered rings
+nR08	number of 8-membered rings
+nR09	number of 9-membered rings
+nR10	number of 10-membered rings
+nR11	number of 11-membered rings
+nR12	number of 12-membered rings
+nBnz	number of benzene-like rings
+ZM1	first Zagreb index M1
+ZM1V	first Zagreb index by valence vertex degrees
+ZM2	second Zagreb index M2
+ZM2V	second Zagreb index by valence vertex degrees
+Qindex	Quadratic index
+SNar	Narumi simple topological index (log)
+HNar	Narumi harmonic topological index
+GNar	Narumi geometric topological index
+Xt	Total structure connectivity index
+Dz	Pogliani index
+Ram	ramification index
+Pol	polarity number
+LPRS	log of product of row sums (PRS)
+VDA	average vertex distance degree
+MSD	mean square distance index (Balaban)
+SMTI	Schultz Molecular Topological Index (MTI)
+SMTIV	Schultz MTI by valence vertex degrees
+GMTI	Gutman Molecular Topological Index
+GMTIV	Gutman MTI by valence vertex degrees
+Xu	Xu index
+SPI	superpendentic index
+W	Wiener W index
+WA	mean Wiener index
+Har	Harary H index
+Har2	square reciprocal distance sum index
+QW	quasi-Wiener index (Kirchhoff number)
+TI1	first Mohar index TI1
+TI2	second Mohar index TI2
+STN	spanning tree number (log)
+HyDp	hyper-distance-path index
+RHyDp	reciprocal hyper-distance-path index
+w	detour index
+ww	hyper-detour index
+Rww	reciprocal hyper-detour index
+D/D	distance/detour index
+Wap	all-path Wiener index
+WhetZ	Wiener-type index from Z weighted distance matrix (Barysz matrix)
+Whetm	Wiener-type index from mass weighted distance matrix
+Whetv	Wiener-type index from van der Waals weighted distance matrix
+Whete	Wiener-type index from electronegativity weighted distance matrix
+Whetp	Wiener-type index from polarizability weighted distance matrix
+J	Balaban distance connectivity index
+JhetZ	Balaban-type index from Z weighted distance matrix (Barysz matrix)
+Jhetm	Balaban-type index from mass weighted distance matrix
+Jhetv	Balaban-type index from van der Waals weighted distance matrix
+Jhete	Balaban-type index from electronegativity weighted distance matrix
+Jhetp	Balaban-type index from polarizability weighted distance matrix
+MAXDN	maximal electrotopological negative variation
+MAXDP	maximal electrotopological positive variation
+DELS	molecular electrotopological variation
+TIE	E-state topological parameter
+S0K	Kier symmetry index
+S1K	1-path Kier alpha-modified shape index
+S2K	2-path Kier alpha-modified shape index
+S3K	3-path Kier alpha-modified shape index
+PHI	Kier flexibility index
+BLI	Kier benzene-likeliness index
+PW2	path/walk 2 - Randic shape index
+PW3	path/walk 3 - Randic shape index
+PW4	path/walk 4 - Randic shape index
+PW5	path/walk 5 - Randic shape index
+PJI2	2D Petitjean shape index
+CSI	eccentric connectivity index
+ECC	eccentricity
+AECC	average eccentricity
+DECC	eccentric
+MDDD	mean distance degree deviation
+UNIP	unipolarity
+CENT	centralization
+VAR	variation
+BAC	Balaban centric index
+Lop	Lopping centric index
+ICR	radial centric information index
+D/Dr03	distance/detour ring index of order 3
+D/Dr04	distance/detour ring index of order 4
+D/Dr05	distance/detour ring index of order 5
+D/Dr06	distance/detour ring index of order 6
+D/Dr07	distance/detour ring index of order 7
+D/Dr08	distance/detour ring index of order 8
+D/Dr09	distance/detour ring index of order 9
+D/Dr10	distance/detour ring index of order 10
+D/Dr11	distance/detour ring index of order 11
+D/Dr12	distance/detour ring index of order 12
+T(N..N)	sum of topological distances between N..N
+T(N..O)	sum of topological distances between N..O
+T(N..S)	sum of topological distances between N..S
+T(N..P)	sum of topological distances between N..P
+T(N..F)	sum of topological distances between N..F
+T(N..Cl)	sum of topological distances between N..Cl
+T(N..Br)	sum of topological distances between N..Br
+T(N..I)	sum of topological distances between N..I
+T(O..O)	sum of topological distances between O..O
+T(O..S)	sum of topological distances between O..S
+T(O..P)	sum of topological distances between O..P
+T(O..F)	sum of topological distances between O..F
+T(O..Cl)	sum of topological distances between O..Cl
+T(O..Br)	sum of topological distances between O..Br
+T(O..I)	sum of topological distances between O..I
+T(S..S)	sum of topological distances between S..S
+T(S..P)	sum of topological distances between S..P
+T(S..F)	sum of topological distances between S..F
+T(S..Cl)	sum of topological distances between S..Cl
+T(S..Br)	sum of topological distances between S..Br
+T(S..I)	sum of topological distances between S..I
+T(P..P)	sum of topological distances between P..P
+T(P..F)	sum of topological distances between P..F
+T(P..Cl)	sum of topological distances between P..Cl
+T(P..Br)	sum of topological distances between P..Br
+T(P..I)	sum of topological distances between P..I
+T(F..F)	sum of topological distances between F..F
+T(F..Cl)	sum of topological distances between F..Cl
+T(F..Br)	sum of topological distances between F..Br
+T(F..I)	sum of topological distances between F..I
+T(Cl..Cl)	sum of topological distances between Cl..Cl
+T(Cl..Br)	sum of topological distances between Cl..Br
+T(Cl..I)	sum of topological distances between Cl..I
+T(Br..Br)	sum of topological distances between Br..Br
+T(Br..I)	sum of topological distances between Br..I
+T(I..I)	sum of topological distances between I..I
+MWC01	molecular walk count of order 01 (number of non-H bonds, nBO)
+MWC02	molecular walk count of order 02
+MWC03	molecular walk count of order 03
+MWC04	molecular walk count of order 04
+MWC05	molecular walk count of order 05
+MWC06	molecular walk count of order 06
+MWC07	molecular walk count of order 07
+MWC08	molecular walk count of order 08
+MWC09	molecular walk count of order 09
+MWC10	molecular walk count of order 10
+TWC	total walk count
+SRW01	self-returning walk count of order 01 (number of non-H atoms, nSK)
+SRW02	self-returning walk count of order 02 (twice the number of non-H bonds)
+SRW03	self-returning walk count of order 03
+SRW04	self-returning walk count of order 04
+SRW05	self-returning walk count of order 05
+SRW06	self-returning walk count of order 06
+SRW07	self-returning walk count of order 07
+SRW08	self-returning walk count of order 08
+SRW09	self-returning walk count of order 09
+SRW10	self-returning walk count of order 10
+MPC01	molecular path count of order 01 (number of non-H bonds, nBO)
+MPC02	molecular path count of order 02 (Gordon-Scantlebury index)
+MPC03	molecular path count of order 03
+MPC04	molecular path count of order 04
+MPC05	molecular path count of order 05
+MPC06	molecular path count of order 06
+MPC07	molecular path count of order 07
+MPC08	molecular path count of order 08
+MPC09	molecular path count of order 09
+MPC10	molecular path count of order 10
+piPC01	molecular multiple path count of order 01 (sum of conventional bond orders, SCBO)
+piPC02	molecular multiple path count of order 02
+piPC03	molecular multiple path count of order 03
+piPC04	molecular multiple path count of order 04
+piPC05	molecular multiple path count of order 05
+piPC06	molecular multiple path count of order 06
+piPC07	molecular multiple path count of order 07
+piPC08	molecular multiple path count of order 08
+piPC09	molecular multiple path count of order 09
+piPC10	molecular multiple path count of order 10
+TPC	total path count
+piID	conventional bond-order ID number
+PCR	ratio of multiple path count over path count
+PCD	difference between multiple path count and path count
+CID	Randic ID number
+BID	Balaban ID number
+ISIZ	information index on molecular size
+IAC	total information index of atomic composition
+AAC	mean information index on atomic composition
+IDE	mean information content on the distance equality
+IDM	mean information content on the distance magnitude
+IDDE	mean information content on the distance degree equality
+IDDM	mean information content on the distance degree magnitude
+IDET	total information content on the distance equality
+IDMT	total information content on the distance magnitude
+IVDE	mean information content on the vertex degree equality
+IVDM	mean information content on the vertex degree magnitude
+HVcpx	graph vertex complexity index
+HDcpx	graph distance complexity index (log)
+Uindex	Balaban U index
+Vindex	Balaban V index
+Xindex	Balaban X index
+Yindex	Balaban Y index
+IC0	information content index (neighborhood symmetry of 0-order)
+TIC0	total information content index (neighborhood symmetry of 0-order)
+SIC0	structural information content (neighborhood symmetry of 0-order)
+CIC0	complementary information content (neighborhood symmetry of 0-order)
+BIC0	bond information content (neighborhood symmetry of 0-order)
+IC1	information content index (neighborhood symmetry of 1-order)
+TIC1	total information content index (neighborhood symmetry of 1-order)
+SIC1	structural information content (neighborhood symmetry of 1-order)
+CIC1	complementary information content (neighborhood symmetry of 1-order)
+BIC1	bond information content (neighborhood symmetry of 1-order)
+IC2	information content index (neighborhood symmetry of 2-order)
+TIC2	total information content index (neighborhood symmetry of 2-order)
+SIC2	structural information content (neighborhood symmetry of 2-order)
+CIC2	complementary information content (neighborhood symmetry of 2-order)
+BIC2	bond information content (neighborhood symmetry of 2-order)
+IC3	information content index (neighborhood symmetry of 3-order)
+TIC3	total information content index (neighborhood symmetry of 3-order)
+SIC3	structural information content (neighborhood symmetry of 3-order)
+CIC3	complementary information content (neighborhood symmetry of 3-order)
+BIC3	bond information content (neighborhood symmetry of 3-order)
+IC4	information content index (neighborhood symmetry of 4-order)
+TIC4	total information content index (neighborhood symmetry of 4-order)
+SIC4	structural information content (neighborhood symmetry of 4-order)
+CIC4	complementary information content (neighborhood symmetry of 4-order)
+BIC4	bond information content (neighborhood symmetry of 4-order)
+IC5	information content index (neighborhood symmetry of 5-order)
+TIC5	total information content index (neighborhood symmetry of 5-order)
+SIC5	structural information content (neighborhood symmetry of 5-order)
+CIC5	complementary information content (neighborhood symmetry of 5-order)
+BIC5	bond information content (neighborhood symmetry of 5-order)
+ATS1m	Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic masses
+ATS2m	Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic masses
+ATS3m	Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic masses
+ATS4m	Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic masses
+ATS5m	Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic masses
+ATS6m	Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic masses
+ATS7m	Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic masses
+ATS8m	Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic masses
+ATS1v	Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic van der Waals volumes
+ATS2v	Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic van der Waals volumes
+ATS3v	Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic van der Waals volumes
+ATS4v	Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic van der Waals volumes
+ATS5v	Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic van der Waals volumes
+ATS6v	Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic van der Waals volumes
+ATS7v	Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic van der Waals volumes
+ATS8v	Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic van der Waals volumes
+ATS1e	Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic Sanderson electronegativities
+ATS2e	Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic Sanderson electronegativities
+ATS3e	Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic Sanderson electronegativities
+ATS4e	Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic Sanderson electronegativities
+ATS5e	Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic Sanderson electronegativities
+ATS6e	Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic Sanderson electronegativities
+ATS7e	Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic Sanderson electronegativities
+ATS8e	Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic Sanderson electronegativities
+ATS1p	Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic polarizabilities
+ATS2p	Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic polarizabilities
+ATS3p	Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic polarizabilities
+ATS4p	Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic polarizabilities
+ATS5p	Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic polarizabilities
+ATS6p	Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic polarizabilities
+ATS7p	Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic polarizabilities
+ATS8p	Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic polarizabilities
+MATS1m	Moran autocorrelation - lag 1 / weighted by atomic masses
+MATS2m	Moran autocorrelation - lag 2 / weighted by atomic masses
+MATS3m	Moran autocorrelation - lag 3 / weighted by atomic masses
+MATS4m	Moran autocorrelation - lag 4 / weighted by atomic masses
+MATS5m	Moran autocorrelation - lag 5 / weighted by atomic masses
+MATS6m	Moran autocorrelation - lag 6 / weighted by atomic masses
+MATS7m	Moran autocorrelation - lag 7 / weighted by atomic masses
+MATS8m	Moran autocorrelation - lag 8 / weighted by atomic masses
+MATS1v	Moran autocorrelation - lag 1 / weighted by atomic van der Waals volumes
+MATS2v	Moran autocorrelation - lag 2 / weighted by atomic van der Waals volumes
+MATS3v	Moran autocorrelation - lag 3 / weighted by atomic van der Waals volumes
+MATS4v	Moran autocorrelation - lag 4 / weighted by atomic van der Waals volumes
+MATS5v	Moran autocorrelation - lag 5 / weighted by atomic van der Waals volumes
+MATS6v	Moran autocorrelation - lag 6 / weighted by atomic van der Waals volumes
+MATS7v	Moran autocorrelation - lag 7 / weighted by atomic van der Waals volumes
+MATS8v	Moran autocorrelation - lag 8 / weighted by atomic van der Waals volumes
+MATS1e	Moran autocorrelation - lag 1 / weighted by atomic Sanderson electronegativities
+MATS2e	Moran autocorrelation - lag 2 / weighted by atomic Sanderson electronegativities
+MATS3e	Moran autocorrelation - lag 3 / weighted by atomic Sanderson electronegativities
+MATS4e	Moran autocorrelation - lag 4 / weighted by atomic Sanderson electronegativities
+MATS5e	Moran autocorrelation - lag 5 / weighted by atomic Sanderson electronegativities
+MATS6e	Moran autocorrelation - lag 6 / weighted by atomic Sanderson electronegativities
+MATS7e	Moran autocorrelation - lag 7 / weighted by atomic Sanderson electronegativities
+MATS8e	Moran autocorrelation - lag 8 / weighted by atomic Sanderson electronegativities
+MATS1p	Moran autocorrelation - lag 1 / weighted by atomic polarizabilities
+MATS2p	Moran autocorrelation - lag 2 / weighted by atomic polarizabilities
+MATS3p	Moran autocorrelation - lag 3 / weighted by atomic polarizabilities
+MATS4p	Moran autocorrelation - lag 4 / weighted by atomic polarizabilities
+MATS5p	Moran autocorrelation - lag 5 / weighted by atomic polarizabilities
+MATS6p	Moran autocorrelation - lag 6 / weighted by atomic polarizabilities
+MATS7p	Moran autocorrelation - lag 7 / weighted by atomic polarizabilities
+MATS8p	Moran autocorrelation - lag 8 / weighted by atomic polarizabilities
+GATS1m	Geary autocorrelation - lag 1 / weighted by atomic masses
+GATS2m	Geary autocorrelation - lag 2 / weighted by atomic masses
+GATS3m	Geary autocorrelation - lag 3 / weighted by atomic masses
+GATS4m	Geary autocorrelation - lag 4 / weighted by atomic masses
+GATS5m	Geary autocorrelation - lag 5 / weighted by atomic masses
+GATS6m	Geary autocorrelation - lag 6 / weighted by atomic masses
+GATS7m	Geary autocorrelation - lag 7 / weighted by atomic masses
+GATS8m	Geary autocorrelation - lag 8 / weighted by atomic masses
+GATS1v	Geary autocorrelation - lag 1 / weighted by atomic van der Waals volumes
+GATS2v	Geary autocorrelation - lag 2 / weighted by atomic van der Waals volumes
+GATS3v	Geary autocorrelation - lag 3 / weighted by atomic van der Waals volumes
+GATS4v	Geary autocorrelation - lag 4 / weighted by atomic van der Waals volumes
+GATS5v	Geary autocorrelation - lag 5 / weighted by atomic van der Waals volumes
+GATS6v	Geary autocorrelation - lag 6 / weighted by atomic van der Waals volumes
+GATS7v	Geary autocorrelation - lag 7 / weighted by atomic van der Waals volumes
+GATS8v	Geary autocorrelation - lag 8 / weighted by atomic van der Waals volumes
+GATS1e	Geary autocorrelation - lag 1 / weighted by atomic Sanderson electronegativities
+GATS2e	Geary autocorrelation - lag 2 / weighted by atomic Sanderson electronegativities
+GATS3e	Geary autocorrelation - lag 3 / weighted by atomic Sanderson electronegativities
+GATS4e	Geary autocorrelation - lag 4 / weighted by atomic Sanderson electronegativities
+GATS5e	Geary autocorrelation - lag 5 / weighted by atomic Sanderson electronegativities
+GATS6e	Geary autocorrelation - lag 6 / weighted by atomic Sanderson electronegativities
+GATS7e	Geary autocorrelation - lag 7 / weighted by atomic Sanderson electronegativities
+GATS8e	Geary autocorrelation - lag 8 / weighted by atomic Sanderson electronegativities
+GATS1p	Geary autocorrelation - lag 1 / weighted by atomic polarizabilities
+GATS2p	Geary autocorrelation - lag 2 / weighted by atomic polarizabilities
+GATS3p	Geary autocorrelation - lag 3 / weighted by atomic polarizabilities
+GATS4p	Geary autocorrelation - lag 4 / weighted by atomic polarizabilities
+GATS5p	Geary autocorrelation - lag 5 / weighted by atomic polarizabilities
+GATS6p	Geary autocorrelation - lag 6 / weighted by atomic polarizabilities
+GATS7p	Geary autocorrelation - lag 7 / weighted by atomic polarizabilities
+GATS8p	Geary autocorrelation - lag 8 / weighted by atomic polarizabilities
+EPS0	edge connectivity index of order 0
+EPS1	edge connectivity index of order 1
+EEig01x	Eigenvalue 01from edge adj. matrix weighted by edge degrees
+EEig02x	Eigenvalue 02from edge adj. matrix weighted by edge degrees
+EEig03x	Eigenvalue 03from edge adj. matrix weighted by edge degrees
+EEig04x	Eigenvalue 04from edge adj. matrix weighted by edge degrees
+EEig05x	Eigenvalue 05from edge adj. matrix weighted by edge degrees
+EEig06x	Eigenvalue 06from edge adj. matrix weighted by edge degrees
+EEig07x	Eigenvalue 07from edge adj. matrix weighted by edge degrees
+EEig08x	Eigenvalue 08from edge adj. matrix weighted by edge degrees
+EEig09x	Eigenvalue 09from edge adj. matrix weighted by edge degrees
+EEig10x	Eigenvalue 10from edge adj. matrix weighted by edge degrees
+EEig11x	Eigenvalue 11from edge adj. matrix weighted by edge degrees
+EEig12x	Eigenvalue 12from edge adj. matrix weighted by edge degrees
+EEig13x	Eigenvalue 13from edge adj. matrix weighted by edge degrees
+EEig14x	Eigenvalue 14from edge adj. matrix weighted by edge degrees
+EEig15x	Eigenvalue 15from edge adj. matrix weighted by edge degrees
+EEig01d	Eigenvalue 01 from edge adj. matrix weighted by dipole moments
+EEig02d	Eigenvalue 02 from edge adj. matrix weighted by dipole moments
+EEig03d	Eigenvalue 03 from edge adj. matrix weighted by dipole moments
+EEig04d	Eigenvalue 04 from edge adj. matrix weighted by dipole moments
+EEig05d	Eigenvalue 05 from edge adj. matrix weighted by dipole moments
+EEig06d	Eigenvalue 06 from edge adj. matrix weighted by dipole moments
+EEig07d	Eigenvalue 07 from edge adj. matrix weighted by dipole moments
+EEig08d	Eigenvalue 08 from edge adj. matrix weighted by dipole moments
+EEig09d	Eigenvalue 09 from edge adj. matrix weighted by dipole moments
+EEig10d	Eigenvalue 10 from edge adj. matrix weighted by dipole moments
+EEig11d	Eigenvalue 11 from edge adj. matrix weighted by dipole moments
+EEig12d	Eigenvalue 12 from edge adj. matrix weighted by dipole moments
+EEig13d	Eigenvalue 13 from edge adj. matrix weighted by dipole moments
+EEig14d	Eigenvalue 14 from edge adj. matrix weighted by dipole moments
+EEig15d	Eigenvalue 15 from edge adj. matrix weighted by dipole moments
+EEig01r	Eigenvalue 01 from edge adj. matrix weighted by resonance integrals
+EEig02r	Eigenvalue 02 from edge adj. matrix weighted by resonance integrals
+EEig03r	Eigenvalue 03 from edge adj. matrix weighted by resonance integrals
+EEig04r	Eigenvalue 04 from edge adj. matrix weighted by resonance integrals
+EEig05r	Eigenvalue 05 from edge adj. matrix weighted by resonance integrals
+EEig06r	Eigenvalue 06 from edge adj. matrix weighted by resonance integrals
+EEig07r	Eigenvalue 07 from edge adj. matrix weighted by resonance integrals
+EEig08r	Eigenvalue 08 from edge adj. matrix weighted by resonance integrals
+EEig09r	Eigenvalue 09 from edge adj. matrix weighted by resonance integrals
+EEig10r	Eigenvalue 10 from edge adj. matrix weighted by resonance integrals
+EEig11r	Eigenvalue 11 from edge adj. matrix weighted by resonance integrals
+EEig12r	Eigenvalue 12 from edge adj. matrix weighted by resonance integrals
+EEig13r	Eigenvalue 13 from edge adj. matrix weighted by resonance integrals
+EEig14r	Eigenvalue 14 from edge adj. matrix weighted by resonance integrals
+EEig15r	Eigenvalue 15 from edge adj. matrix weighted by resonance integrals
+ESpm01u	Spectral moment 01 from edge adj. matrix
+ESpm02u	Spectral moment 02 from edge adj. matrix
+ESpm03u	Spectral moment 03 from edge adj. matrix
+ESpm04u	Spectral moment 04 from edge adj. matrix
+ESpm05u	Spectral moment 05 from edge adj. matrix
+ESpm06u	Spectral moment 06 from edge adj. matrix
+ESpm07u	Spectral moment 07 from edge adj. matrix
+ESpm08u	Spectral moment 08 from edge adj. matrix
+ESpm09u	Spectral moment 09 from edge adj. matrix
+ESpm10u	Spectral moment 10 from edge adj. matrix
+ESpm11u	Spectral moment 11 from edge adj. matrix
+ESpm12u	Spectral moment 12 from edge adj. matrix
+ESpm13u	Spectral moment 13 from edge adj. matrix
+ESpm14u	Spectral moment 14 from edge adj. matrix
+ESpm15u	Spectral moment 15 from edge adj. matrix
+ESpm01x	Spectral moment 01 from edge adj. matrix weighted by edge degrees
+ESpm02x	Spectral moment 02 from edge adj. matrix weighted by edge degrees
+ESpm03x	Spectral moment 03 from edge adj. matrix weighted by edge degrees
+ESpm04x	Spectral moment 04 from edge adj. matrix weighted by edge degrees
+ESpm05x	Spectral moment 05 from edge adj. matrix weighted by edge degrees
+ESpm06x	Spectral moment 06 from edge adj. matrix weighted by edge degrees
+ESpm07x	Spectral moment 07 from edge adj. matrix weighted by edge degrees
+ESpm08x	Spectral moment 08 from edge adj. matrix weighted by edge degrees
+ESpm09x	Spectral moment 09 from edge adj. matrix weighted by edge degrees
+ESpm10x	Spectral moment 10 from edge adj. matrix weighted by edge degrees
+ESpm11x	Spectral moment 11 from edge adj. matrix weighted by edge degrees
+ESpm12x	Spectral moment 12 from edge adj. matrix weighted by edge degrees
+ESpm13x	Spectral moment 13 from edge adj. matrix weighted by edge degrees
+ESpm14x	Spectral moment 14 from edge adj. matrix weighted by edge degrees
+ESpm15x	Spectral moment 15 from edge adj. matrix weighted by edge degrees
+ESpm01d	Spectral moment 01 from edge adj. matrix weighted by dipole moments
+ESpm02d	Spectral moment 02 from edge adj. matrix weighted by dipole moments
+ESpm03d	Spectral moment 03 from edge adj. matrix weighted by dipole moments
+ESpm04d	Spectral moment 04 from edge adj. matrix weighted by dipole moments
+ESpm05d	Spectral moment 05 from edge adj. matrix weighted by dipole moments
+ESpm06d	Spectral moment 06 from edge adj. matrix weighted by dipole moments
+ESpm07d	Spectral moment 07 from edge adj. matrix weighted by dipole moments
+ESpm08d	Spectral moment 08 from edge adj. matrix weighted by dipole moments
+ESpm09d	Spectral moment 09 from edge adj. matrix weighted by dipole moments
+ESpm10d	Spectral moment 10 from edge adj. matrix weighted by dipole moments
+ESpm11d	Spectral moment 11 from edge adj. matrix weighted by dipole moments
+ESpm12d	Spectral moment 12 from edge adj. matrix weighted by dipole moments
+ESpm13d	Spectral moment 13 from edge adj. matrix weighted by dipole moments
+ESpm14d	Spectral moment 14 from edge adj. matrix weighted by dipole moments
+ESpm15d	Spectral moment 15 from edge adj. matrix weighted by dipole moments
+ESpm01r	Spectral moment 01 from edge adj. matrix weighted by resonance integrals
+ESpm02r	Spectral moment 02 from edge adj. matrix weighted by resonance integrals
+ESpm03r	Spectral moment 03 from edge adj. matrix weighted by resonance integrals
+ESpm04r	Spectral moment 04 from edge adj. matrix weighted by resonance integrals
+ESpm05r	Spectral moment 05 from edge adj. matrix weighted by resonance integrals
+ESpm06r	Spectral moment 06 from edge adj. matrix weighted by resonance integrals
+ESpm07r	Spectral moment 07 from edge adj. matrix weighted by resonance integrals
+ESpm08r	Spectral moment 08 from edge adj. matrix weighted by resonance integrals
+ESpm09r	Spectral moment 09 from edge adj. matrix weighted by resonance integrals
+ESpm10r	Spectral moment 10 from edge adj. matrix weighted by resonance integrals
+ESpm11r	Spectral moment 11 from edge adj. matrix weighted by resonance integrals
+ESpm12r	Spectral moment 12 from edge adj. matrix weighted by resonance integrals
+ESpm13r	Spectral moment 13 from edge adj. matrix weighted by resonance integrals
+ESpm14r	Spectral moment 14 from edge adj. matrix weighted by resonance integrals
+ESpm15r	Spectral moment 15 from edge adj. matrix weighted by resonance integrals
+BEHm1	highest eigenvalue n. 1 of Burden matrix / weighted by atomic masses
+BEHm2	highest eigenvalue n. 2 of Burden matrix / weighted by atomic masses
+BEHm3	highest eigenvalue n. 3 of Burden matrix / weighted by atomic masses
+BEHm4	highest eigenvalue n. 4 of Burden matrix / weighted by atomic masses
+BEHm5	highest eigenvalue n. 5 of Burden matrix / weighted by atomic masses
+BEHm6	highest eigenvalue n. 6 of Burden matrix / weighted by atomic masses
+BEHm7	highest eigenvalue n. 7 of Burden matrix / weighted by atomic masses
+BEHm8	highest eigenvalue n. 8 of Burden matrix / weighted by atomic masses
+BELm1	lowest eigenvalue n. 1 of Burden matrix / weighted by atomic masses
+BELm2	lowest eigenvalue n. 2 of Burden matrix / weighted by atomic masses
+BELm3	lowest eigenvalue n. 3 of Burden matrix / weighted by atomic masses
+BELm4	lowest eigenvalue n. 4 of Burden matrix / weighted by atomic masses
+BELm5	lowest eigenvalue n. 5 of Burden matrix / weighted by atomic masses
+BELm6	lowest eigenvalue n. 6 of Burden matrix / weighted by atomic masses
+BELm7	lowest eigenvalue n. 7 of Burden matrix / weighted by atomic masses
+BELm8	lowest eigenvalue n. 8 of Burden matrix / weighted by atomic masses
+BEHv1	highest eigenvalue n. 1 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv2	highest eigenvalue n. 2 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv3	highest eigenvalue n. 3 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv4	highest eigenvalue n. 4 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv5	highest eigenvalue n. 5 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv6	highest eigenvalue n. 6 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv7	highest eigenvalue n. 7 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv8	highest eigenvalue n. 8 of Burden matrix / weighted by atomic van der Waals volumes
+BELv1	lowest eigenvalue n. 1 of Burden matrix / weighted by atomic van der Waals volumes
+BELv2	lowest eigenvalue n. 2 of Burden matrix / weighted by atomic van der Waals volumes
+BELv3	lowest eigenvalue n. 3 of Burden matrix / weighted by atomic van der Waals volumes
+BELv4	lowest eigenvalue n. 4 of Burden matrix / weighted by atomic van der Waals volumes
+BELv5	lowest eigenvalue n. 5 of Burden matrix / weighted by atomic van der Waals volumes
+BELv6	lowest eigenvalue n. 6 of Burden matrix / weighted by atomic van der Waals volumes
+BELv7	lowest eigenvalue n. 7 of Burden matrix / weighted by atomic van der Waals volumes
+BELv8	lowest eigenvalue n. 8 of Burden matrix / weighted by atomic van der Waals volumes
+BEHe1	highest eigenvalue n. 1 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe2	highest eigenvalue n. 2 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe3	highest eigenvalue n. 3 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe4	highest eigenvalue n. 4 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe5	highest eigenvalue n. 5 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe6	highest eigenvalue n. 6 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe7	highest eigenvalue n. 7 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe8	highest eigenvalue n. 8 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe1	lowest eigenvalue n. 1 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe2	lowest eigenvalue n. 2 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe3	lowest eigenvalue n. 3 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe4	lowest eigenvalue n. 4 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe5	lowest eigenvalue n. 5 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe6	lowest eigenvalue n. 6 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe7	lowest eigenvalue n. 7 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe8	lowest eigenvalue n. 8 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHp1	highest eigenvalue n. 1 of Burden matrix / weighted by atomic polarizabilities
+BEHp2	highest eigenvalue n. 2 of Burden matrix / weighted by atomic polarizabilities
+BEHp3	highest eigenvalue n. 3 of Burden matrix / weighted by atomic polarizabilities
+BEHp4	highest eigenvalue n. 4 of Burden matrix / weighted by atomic polarizabilities
+BEHp5	highest eigenvalue n. 5 of Burden matrix / weighted by atomic polarizabilities
+BEHp6	highest eigenvalue n. 6 of Burden matrix / weighted by atomic polarizabilities
+BEHp7	highest eigenvalue n. 7 of Burden matrix / weighted by atomic polarizabilities
+BEHp8	highest eigenvalue n. 8 of Burden matrix / weighted by atomic polarizabilities
+BELp1	lowest eigenvalue n. 1 of Burden matrix / weighted by atomic polarizabilities
+BELp2	lowest eigenvalue n. 2 of Burden matrix / weighted by atomic polarizabilities
+BELp3	lowest eigenvalue n. 3 of Burden matrix / weighted by atomic polarizabilities
+BELp4	lowest eigenvalue n. 4 of Burden matrix / weighted by atomic polarizabilities
+BELp5	lowest eigenvalue n. 5 of Burden matrix / weighted by atomic polarizabilities
+BELp6	lowest eigenvalue n. 6 of Burden matrix / weighted by atomic polarizabilities
+BELp7	lowest eigenvalue n. 7 of Burden matrix / weighted by atomic polarizabilities
+BELp8	lowest eigenvalue n. 8 of Burden matrix / weighted by atomic polarizabilities
+GGI1	topological charge index of order 1
+GGI2	topological charge index of order 2
+GGI3	topological charge index of order 3
+GGI4	topological charge index of order 4
+GGI5	topological charge index of order 5
+GGI6	topological charge index of order 6
+GGI7	topological charge index of order 7
+GGI8	topological charge index of order 8
+GGI9	topological charge index of order 9
+GGI10	topological charge index of order 10
+JGI1	mean topological charge index of order1
+JGI2	mean topological charge index of order2
+JGI3	mean topological charge index of order3
+JGI4	mean topological charge index of order4
+JGI5	mean topological charge index of order5
+JGI6	mean topological charge index of order6
+JGI7	mean topological charge index of order7
+JGI8	mean topological charge index of order8
+JGI9	mean topological charge index of order9
+JGI10	mean topological charge index of order10
+JGT	global topological charge index
+LP1	Lovasz-Pelikan index (leading eigenvalue)
+Eig1Z	Leading eigenvalue from Z weighted distance matrix (Barysz matrix)
+Eig1m	Leading eigenvalue from mass weighted distance matrix
+Eig1v	Leading eigenvalue from van der Waals weighted distance matrix
+Eig1e	Leading eigenvalue from electronegativity weighted distance matrix
+Eig1p	Leading eigenvalue from polarizability weighted distance matrix
+SEigZ	Eigenvalue sum from Z weighted distance matrix (Barysz matrix)
+SEigm	Eigenvalue sum from mass weighted distance matrix
+SEigv	Eigenvalue sum from van der Waals weighted distance matrix
+SEige	Eigenvalue sum from electronegativity weighted distance matrix
+SEigp	Eigenvalue sum from polarizability weighted distance matrix
+AEigZ	Absolute eigenvalue sum from Z weighted distance matrix (Barysz matrix)
+AEigm	Absolute eigenvalue sum from mass weighted distance matrix
+AEigv	Absolute eigenvalue sum from van der Waals weighted distance matrix
+AEige	Absolute eigenvalue sum from electronegativity weighted distance matrix
+AEigp	Absolute eigenvalue sum from polarizability weighted distance matrix
+VEA1	eigenvector coefficient sum from adjacency matrix
+VEA2	average eigenvector coefficient sum from adjacency matrix
+VRA1	Randic-type eigenvector-based index from adjacency matrix
+VRA2	average Randic-type eigenvector-based index from adjacency matrix
+VED1	eigenvector coefficient sum from distance matrix
+VED2	average eigenvector coefficient sum from distance matrix
+VRD1	Randic-type eigenvector-based index from distance matrix
+VRD2	average Randic-type eigenvector-based index from distance matrix
+VEZ1	eigenvector coefficient sum from Z weighted distance matrix (Barysz matrix)
+VEZ2	average eigenvector coefficient sum from Z weighted distance matrix (Barysz matrix)
+VRZ1	Randic-type eigenvector-based index from Z weighted distance matrix (Barysz matrix)
+VRZ2	average Randic-type eigenvector-based index from Z weighted distance matrix (Barysz matrix)
+VEm1	eigenvector coefficient sum from mass weighted distance matrix
+VEm2	average eigenvector coefficient sum from mass weighted distance matrix
+VRm1	Randic-type eigenvector-based index from mass weighted distance matrix
+VRm2	average Randic-type eigenvector-based index from mass weighted distance matrix
+VEv1	eigenvector coefficient sum from van der Waals weighted distance matrix
+VEv2	average eigenvector coefficient sum from van der Waals weighted distance matrix
+VRv1	Randic-type eigenvector-based index from van der Waals weighted distance matrix
+VRv2	average Randic-type eigenvector-based index from van der Waals weighted distance matrix
+VEe1	eigenvector coefficient sum from electronegativity weighted distance matrix
+VEe2	average eigenvector coefficient sum from electronegativity weighted distance matrix
+VRe1	Randic-type eigenvector-based index from electronegativity weighted distance matrix
+VRe2	average Randic-type eigenvector-based index from electronegativity weighted distance matrix
+VEp1	eigenvector coefficient sum from polarizability weighted distance matrix
+VEp2	average eigenvector coefficient sum from polarizability weighted distance matrix
+VRp1	Randic-type eigenvector-based index from polarizability weighted distance matrix
+VRp2	average Randic-type eigenvector-based index from polarizability weighted distance matrix
+DP01	molecular profile no. 01
+DP02	molecular profile no. 02
+DP03	molecular profile no. 03
+DP04	molecular profile no. 04
+DP05	molecular profile no. 05
+DP06	molecular profile no. 06
+DP07	molecular profile no. 07
+DP08	molecular profile no. 08
+DP09	molecular profile no. 09
+DP10	molecular profile no. 10
+DP11	molecular profile no. 11
+DP12	molecular profile no. 12
+DP13	molecular profile no. 13
+DP14	molecular profile no. 14
+DP15	molecular profile no. 15
+DP16	molecular profile no. 16
+DP17	molecular profile no. 17
+DP18	molecular profile no. 18
+DP19	molecular profile no. 19
+DP20	molecular profile no. 20
+SP01	shape profile no. 01
+SP02	shape profile no. 02
+SP03	shape profile no. 03
+SP04	shape profile no. 04
+SP05	shape profile no. 05
+SP06	shape profile no. 06
+SP07	shape profile no. 07
+SP08	shape profile no. 08
+SP09	shape profile no. 09
+SP10	shape profile no. 10
+SP11	shape profile no. 11
+SP12	shape profile no. 12
+SP13	shape profile no. 13
+SP14	shape profile no. 14
+SP15	shape profile no. 15
+SP16	shape profile no. 16
+SP17	shape profile no. 17
+SP18	shape profile no. 18
+SP19	shape profile no. 19
+SP20	shape profile no. 20
+SHP2	average shape profile index of order 2
+W3D	3D-Wiener index
+J3D	3D-Balaban index
+H3D	3D-Harary index
+AGDD	average geometric distance degree
+DDI	D/D index
+ADDD	average distance/distance degree
+G1	gravitational index G1
+G2	gravitational index G2 (bond-restricted)
+RGyr	radius of gyration (mass weighted)
+SPAN	span R
+SPAM	average span R
+MEcc	molecular eccentricity
+SPH	spherosity
+ASP	asphericity
+FDI	folding degree index
+PJI3	3D Petijean shape index
+L/Bw	length-to-breadth ratio by WHIM
+SEig	absolute eigenvalue sum on geometry matrix
+HOMA	Harmonic Oscillator Model of Aromaticity index
+RCI	Jug RC index
+AROM	aromaticity (trial)
+HOMT	HOMA total (trial)
+DISPm	d COMMA2 value / weighted by atomic masses
+QXXm	Qxx COMMA2 value / weighted by atomic masses
+QYYm	Qyy COMMA2 value / weighted by atomic masses
+QZZm	Qzz COMMA2 value / weighted by atomic masses
+DISPv	d COMMA2 value / weighted by atomic van der Waals volumes
+QXXv	Qxx COMMA2 value / weighted by atomic van der Waals volumes
+QYYv	Qyy COMMA2 value / weighted by atomic van der Waals volumes
+QZZv	Qzz COMMA2 value / weighted by atomic van der Waals volumes
+DISPe	d COMMA2 value / weighted by atomic Sanderson electronegativities
+QXXe	Qxx COMMA2 value / weighted by atomic Sanderson electronegativities
+QYYe	Qyy COMMA2 value / weighted by atomic Sanderson electronegativities
+QZZe	Qzz COMMA2 value / weighted by atomic Sanderson electronegativities
+DISPp	d COMMA2 value / weighted by atomic polarizabilities
+QXXp	Qxx COMMA2 value / weighted by atomic polarizabilities
+QYYp	Qyy COMMA2 value / weighted by atomic polarizabilities
+QZZp	Qzz COMMA2 value / weighted by atomic polarizabilities
+G(N..N)	sum of geometrical distances between N..N
+G(N..O)	sum of geometrical distances between N..O
+G(N..S)	sum of geometrical distances between N..S
+G(N..P)	sum of geometrical distances between N..P
+G(N..F)	sum of geometrical distances between N..F
+G(N..Cl)	sum of geometrical distances between N..Cl
+G(N..Br)	sum of geometrical distances between N..Br
+G(N..I)	sum of geometrical distances between N..I
+G(O..O)	sum of geometrical distances between O..O
+G(O..S)	sum of geometrical distances between O..S
+G(O..P)	sum of geometrical distances between O..P
+G(O..F)	sum of geometrical distances between O..F
+G(O..Cl)	sum of geometrical distances between O..Cl
+G(O..Br)	sum of geometrical distances between O..Br
+G(O..I)	sum of geometrical distances between O..I
+G(S..S)	sum of geometrical distances between S..S
+G(S..P)	sum of geometrical distances between S..P
+G(S..F)	sum of geometrical distances between S..F
+G(S..Cl)	sum of geometrical distances between S..Cl
+G(S..Br)	sum of geometrical distances between S..Br
+G(S..I)	sum of geometrical distances between S..I
+G(P..P)	sum of geometrical distances between P..P
+G(P..F)	sum of geometrical distances between P..F
+G(P..Cl)	sum of geometrical distances between P..Cl
+G(P..Br)	sum of geometrical distances between P..Br
+G(P..I)	sum of geometrical distances between P..I
+G(F..F)	sum of geometrical distances between F..F
+G(F..Cl)	sum of geometrical distances between F..Cl
+G(F..Br)	sum of geometrical distances between F..Br
+G(F..I)	sum of geometrical distances between F..I
+G(Cl..Cl)	sum of geometrical distances between Cl..Cl
+G(Cl..Br)	sum of geometrical distances between Cl..Br
+G(Cl..I)	sum of geometrical distances between Cl..I
+G(Br..Br)	sum of geometrical distances between Br..Br
+G(Br..I)	sum of geometrical distances between Br..I
+G(I..I)	sum of geometrical distances between I..I
+RDF010u	Radial Distribution Function - 1.0 / unweighted
+RDF015u	Radial Distribution Function - 1.5 / unweighted
+RDF020u	Radial Distribution Function - 2.0 / unweighted
+RDF025u	Radial Distribution Function - 2.5 / unweighted
+RDF030u	Radial Distribution Function - 3.0 / unweighted
+RDF035u	Radial Distribution Function - 3.5 / unweighted
+RDF040u	Radial Distribution Function - 4.0 / unweighted
+RDF045u	Radial Distribution Function - 4.5 / unweighted
+RDF050u	Radial Distribution Function - 5.0 / unweighted
+RDF055u	Radial Distribution Function - 5.5 / unweighted
+RDF060u	Radial Distribution Function - 6.0 / unweighted
+RDF065u	Radial Distribution Function - 6.5 / unweighted
+RDF070u	Radial Distribution Function - 7.0 / unweighted
+RDF075u	Radial Distribution Function - 7.5 / unweighted
+RDF080u	Radial Distribution Function - 8.0 / unweighted
+RDF085u	Radial Distribution Function - 8.5 / unweighted
+RDF090u	Radial Distribution Function - 9.0 / unweighted
+RDF095u	Radial Distribution Function - 9.5 / unweighted
+RDF100u	Radial Distribution Function - 10.0 / unweighted
+RDF105u	Radial Distribution Function - 10.5 / unweighted
+RDF110u	Radial Distribution Function - 11.0 / unweighted
+RDF115u	Radial Distribution Function - 11.5 / unweighted
+RDF120u	Radial Distribution Function - 12.0 / unweighted
+RDF125u	Radial Distribution Function - 12.5 / unweighted
+RDF130u	Radial Distribution Function - 13.0 / unweighted
+RDF135u	Radial Distribution Function - 13.5 / unweighted
+RDF140u	Radial Distribution Function - 14.0 / unweighted
+RDF145u	Radial Distribution Function - 14.5 / unweighted
+RDF150u	Radial Distribution Function - 15.0 / unweighted
+RDF155u	Radial Distribution Function - 15.5 / unweighted
+RDF010m	Radial Distribution Function - 1.0 / weighted by atomic masses
+RDF015m	Radial Distribution Function - 1.5 / weighted by atomic masses
+RDF020m	Radial Distribution Function - 2.0 / weighted by atomic masses
+RDF025m	Radial Distribution Function - 2.5 / weighted by atomic masses
+RDF030m	Radial Distribution Function - 3.0 / weighted by atomic masses
+RDF035m	Radial Distribution Function - 3.5 / weighted by atomic masses
+RDF040m	Radial Distribution Function - 4.0 / weighted by atomic masses
+RDF045m	Radial Distribution Function - 4.5 / weighted by atomic masses
+RDF050m	Radial Distribution Function - 5.0 / weighted by atomic masses
+RDF055m	Radial Distribution Function - 5.5 / weighted by atomic masses
+RDF060m	Radial Distribution Function - 6.0 / weighted by atomic masses
+RDF065m	Radial Distribution Function - 6.5 / weighted by atomic masses
+RDF070m	Radial Distribution Function - 7.0 / weighted by atomic masses
+RDF075m	Radial Distribution Function - 7.5 / weighted by atomic masses
+RDF080m	Radial Distribution Function - 8.0 / weighted by atomic masses
+RDF085m	Radial Distribution Function - 8.5 / weighted by atomic masses
+RDF090m	Radial Distribution Function - 9.0 / weighted by atomic masses
+RDF095m	Radial Distribution Function - 9.5 / weighted by atomic masses
+RDF100m	Radial Distribution Function - 10.0 / weighted by atomic masses
+RDF105m	Radial Distribution Function - 10.5 / weighted by atomic masses
+RDF110m	Radial Distribution Function - 11.0 / weighted by atomic masses
+RDF115m	Radial Distribution Function - 11.5 / weighted by atomic masses
+RDF120m	Radial Distribution Function - 12.0 / weighted by atomic masses
+RDF125m	Radial Distribution Function - 12.5 / weighted by atomic masses
+RDF130m	Radial Distribution Function - 13.0 / weighted by atomic masses
+RDF135m	Radial Distribution Function - 13.5 / weighted by atomic masses
+RDF140m	Radial Distribution Function - 14.0 / weighted by atomic masses
+RDF145m	Radial Distribution Function - 14.5 / weighted by atomic masses
+RDF150m	Radial Distribution Function - 15.0 / weighted by atomic masses
+RDF155m	Radial Distribution Function - 15.5 / weighted by atomic masses
+RDF010v	Radial Distribution Function - 1.0 / weighted by atomic van der Waals volumes
+RDF015v	Radial Distribution Function - 1.5 / weighted by atomic van der Waals volumes
+RDF020v	Radial Distribution Function - 2.0 / weighted by atomic van der Waals volumes
+RDF025v	Radial Distribution Function - 2.5 / weighted by atomic van der Waals volumes
+RDF030v	Radial Distribution Function - 3.0 / weighted by atomic van der Waals volumes
+RDF035v	Radial Distribution Function - 3.5 / weighted by atomic van der Waals volumes
+RDF040v	Radial Distribution Function - 4.0 / weighted by atomic van der Waals volumes
+RDF045v	Radial Distribution Function - 4.5 / weighted by atomic van der Waals volumes
+RDF050v	Radial Distribution Function - 5.0 / weighted by atomic van der Waals volumes
+RDF055v	Radial Distribution Function - 5.5 / weighted by atomic van der Waals volumes
+RDF060v	Radial Distribution Function - 6.0 / weighted by atomic van der Waals volumes
+RDF065v	Radial Distribution Function - 6.5 / weighted by atomic van der Waals volumes
+RDF070v	Radial Distribution Function - 7.0 / weighted by atomic van der Waals volumes
+RDF075v	Radial Distribution Function - 7.5 / weighted by atomic van der Waals volumes
+RDF080v	Radial Distribution Function - 8.0 / weighted by atomic van der Waals volumes
+RDF085v	Radial Distribution Function - 8.5 / weighted by atomic van der Waals volumes
+RDF090v	Radial Distribution Function - 9.0 / weighted by atomic van der Waals volumes
+RDF095v	Radial Distribution Function - 9.5 / weighted by atomic van der Waals volumes
+RDF100v	Radial Distribution Function - 10.0 / weighted by atomic van der Waals volumes
+RDF105v	Radial Distribution Function - 10.5 / weighted by atomic van der Waals volumes
+RDF110v	Radial Distribution Function - 11.0 / weighted by atomic van der Waals volumes
+RDF115v	Radial Distribution Function - 11.5 / weighted by atomic van der Waals volumes
+RDF120v	Radial Distribution Function - 12.0 / weighted by atomic van der Waals volumes
+RDF125v	Radial Distribution Function - 12.5 / weighted by atomic van der Waals volumes
+RDF130v	Radial Distribution Function - 13.0 / weighted by atomic van der Waals volumes
+RDF135v	Radial Distribution Function - 13.5 / weighted by atomic van der Waals volumes
+RDF140v	Radial Distribution Function - 14.0 / weighted by atomic van der Waals volumes
+RDF145v	Radial Distribution Function - 14.5 / weighted by atomic van der Waals volumes
+RDF150v	Radial Distribution Function - 15.0 / weighted by atomic van der Waals volumes
+RDF155v	Radial Distribution Function - 15.5 / weighted by atomic van der Waals volumes
+RDF010e	Radial Distribution Function - 1.0 / weighted by atomic Sanderson electronegativities
+RDF015e	Radial Distribution Function - 1.5 / weighted by atomic Sanderson electronegativities
+RDF020e	Radial Distribution Function - 2.0 / weighted by atomic Sanderson electronegativities
+RDF025e	Radial Distribution Function - 2.5 / weighted by atomic Sanderson electronegativities
+RDF030e	Radial Distribution Function - 3.0 / weighted by atomic Sanderson electronegativities
+RDF035e	Radial Distribution Function - 3.5 / weighted by atomic Sanderson electronegativities
+RDF040e	Radial Distribution Function - 4.0 / weighted by atomic Sanderson electronegativities
+RDF045e	Radial Distribution Function - 4.5 / weighted by atomic Sanderson electronegativities
+RDF050e	Radial Distribution Function - 5.0 / weighted by atomic Sanderson electronegativities
+RDF055e	Radial Distribution Function - 5.5 / weighted by atomic Sanderson electronegativities
+RDF060e	Radial Distribution Function - 6.0 / weighted by atomic Sanderson electronegativities
+RDF065e	Radial Distribution Function - 6.5 / weighted by atomic Sanderson electronegativities
+RDF070e	Radial Distribution Function - 7.0 / weighted by atomic Sanderson electronegativities
+RDF075e	Radial Distribution Function - 7.5 / weighted by atomic Sanderson electronegativities
+RDF080e	Radial Distribution Function - 8.0 / weighted by atomic Sanderson electronegativities
+RDF085e	Radial Distribution Function - 8.5 / weighted by atomic Sanderson electronegativities
+RDF090e	Radial Distribution Function - 9.0 / weighted by atomic Sanderson electronegativities
+RDF095e	Radial Distribution Function - 9.5 / weighted by atomic Sanderson electronegativities
+RDF100e	Radial Distribution Function - 10.0 / weighted by atomic Sanderson electronegativities
+RDF105e	Radial Distribution Function - 10.5 / weighted by atomic Sanderson electronegativities
+RDF110e	Radial Distribution Function - 11.0 / weighted by atomic Sanderson electronegativities
+RDF115e	Radial Distribution Function - 11.5 / weighted by atomic Sanderson electronegativities
+RDF120e	Radial Distribution Function - 12.0 / weighted by atomic Sanderson electronegativities
+RDF125e	Radial Distribution Function - 12.5 / weighted by atomic Sanderson electronegativities
+RDF130e	Radial Distribution Function - 13.0 / weighted by atomic Sanderson electronegativities
+RDF135e	Radial Distribution Function - 13.5 / weighted by atomic Sanderson electronegativities
+RDF140e	Radial Distribution Function - 14.0 / weighted by atomic Sanderson electronegativities
+RDF145e	Radial Distribution Function - 14.5 / weighted by atomic Sanderson electronegativities
+RDF150e	Radial Distribution Function - 15.0 / weighted by atomic Sanderson electronegativities
+RDF155e	Radial Distribution Function - 15.5 / weighted by atomic Sanderson electronegativities
+RDF010p	Radial Distribution Function - 1.0 / weighted by atomic polarizabilities
+RDF015p	Radial Distribution Function - 1.5 / weighted by atomic polarizabilities
+RDF020p	Radial Distribution Function - 2.0 / weighted by atomic polarizabilities
+RDF025p	Radial Distribution Function - 2.5 / weighted by atomic polarizabilities
+RDF030p	Radial Distribution Function - 3.0 / weighted by atomic polarizabilities
+RDF035p	Radial Distribution Function - 3.5 / weighted by atomic polarizabilities
+RDF040p	Radial Distribution Function - 4.0 / weighted by atomic polarizabilities
+RDF045p	Radial Distribution Function - 4.5 / weighted by atomic polarizabilities
+RDF050p	Radial Distribution Function - 5.0 / weighted by atomic polarizabilities
+RDF055p	Radial Distribution Function - 5.5 / weighted by atomic polarizabilities
+RDF060p	Radial Distribution Function - 6.0 / weighted by atomic polarizabilities
+RDF065p	Radial Distribution Function - 6.5 / weighted by atomic polarizabilities
+RDF070p	Radial Distribution Function - 7.0 / weighted by atomic polarizabilities
+RDF075p	Radial Distribution Function - 7.5 / weighted by atomic polarizabilities
+RDF080p	Radial Distribution Function - 8.0 / weighted by atomic polarizabilities
+RDF085p	Radial Distribution Function - 8.5 / weighted by atomic polarizabilities
+RDF090p	Radial Distribution Function - 9.0 / weighted by atomic polarizabilities
+RDF095p	Radial Distribution Function - 9.5 / weighted by atomic polarizabilities
+RDF100p	Radial Distribution Function - 10.0 / weighted by atomic polarizabilities
+RDF105p	Radial Distribution Function - 10.5 / weighted by atomic polarizabilities
+RDF110p	Radial Distribution Function - 11.0 / weighted by atomic polarizabilities
+RDF115p	Radial Distribution Function - 11.5 / weighted by atomic polarizabilities
+RDF120p	Radial Distribution Function - 12.0 / weighted by atomic polarizabilities
+RDF125p	Radial Distribution Function - 12.5 / weighted by atomic polarizabilities
+RDF130p	Radial Distribution Function - 13.0 / weighted by atomic polarizabilities
+RDF135p	Radial Distribution Function - 13.5 / weighted by atomic polarizabilities
+RDF140p	Radial Distribution Function - 14.0 / weighted by atomic polarizabilities
+RDF145p	Radial Distribution Function - 14.5 / weighted by atomic polarizabilities
+RDF150p	Radial Distribution Function - 15.0 / weighted by atomic polarizabilities
+RDF155p	Radial Distribution Function - 15.5 / weighted by atomic polarizabilities
+Mor01u	3D-MoRSE - signal 01 / unweighted
+Mor02u	3D-MoRSE - signal 02 / unweighted
+Mor03u	3D-MoRSE - signal 03 / unweighted
+Mor04u	3D-MoRSE - signal 04 / unweighted
+Mor05u	3D-MoRSE - signal 05 / unweighted
+Mor06u	3D-MoRSE - signal 06 / unweighted
+Mor07u	3D-MoRSE - signal 07 / unweighted
+Mor08u	3D-MoRSE - signal 08 / unweighted
+Mor09u	3D-MoRSE - signal 09 / unweighted
+Mor10u	3D-MoRSE - signal 10 / unweighted
+Mor11u	3D-MoRSE - signal 11 / unweighted
+Mor12u	3D-MoRSE - signal 12 / unweighted
+Mor13u	3D-MoRSE - signal 13 / unweighted
+Mor14u	3D-MoRSE - signal 14 / unweighted
+Mor15u	3D-MoRSE - signal 15 / unweighted
+Mor16u	3D-MoRSE - signal 16 / unweighted
+Mor17u	3D-MoRSE - signal 17 / unweighted
+Mor18u	3D-MoRSE - signal 18 / unweighted
+Mor19u	3D-MoRSE - signal 19 / unweighted
+Mor20u	3D-MoRSE - signal 20 / unweighted
+Mor21u	3D-MoRSE - signal 21 / unweighted
+Mor22u	3D-MoRSE - signal 22 / unweighted
+Mor23u	3D-MoRSE - signal 23 / unweighted
+Mor24u	3D-MoRSE - signal 24 / unweighted
+Mor25u	3D-MoRSE - signal 25 / unweighted
+Mor26u	3D-MoRSE - signal 26 / unweighted
+Mor27u	3D-MoRSE - signal 27 / unweighted
+Mor28u	3D-MoRSE - signal 28 / unweighted
+Mor29u	3D-MoRSE - signal 29 / unweighted
+Mor30u	3D-MoRSE - signal 30 / unweighted
+Mor31u	3D-MoRSE - signal 31 / unweighted
+Mor32u	3D-MoRSE - signal 32 / unweighted
+Mor01m	3D-MoRSE - signal 01 / weighted by atomic masses
+Mor02m	3D-MoRSE - signal 02 / weighted by atomic masses
+Mor03m	3D-MoRSE - signal 03 / weighted by atomic masses
+Mor04m	3D-MoRSE - signal 04 / weighted by atomic masses
+Mor05m	3D-MoRSE - signal 05 / weighted by atomic masses
+Mor06m	3D-MoRSE - signal 06 / weighted by atomic masses
+Mor07m	3D-MoRSE - signal 07 / weighted by atomic masses
+Mor08m	3D-MoRSE - signal 08 / weighted by atomic masses
+Mor09m	3D-MoRSE - signal 09 / weighted by atomic masses
+Mor10m	3D-MoRSE - signal 10 / weighted by atomic masses
+Mor11m	3D-MoRSE - signal 11 / weighted by atomic masses
+Mor12m	3D-MoRSE - signal 12 / weighted by atomic masses
+Mor13m	3D-MoRSE - signal 13 / weighted by atomic masses
+Mor14m	3D-MoRSE - signal 14 / weighted by atomic masses
+Mor15m	3D-MoRSE - signal 15 / weighted by atomic masses
+Mor16m	3D-MoRSE - signal 16 / weighted by atomic masses
+Mor17m	3D-MoRSE - signal 17 / weighted by atomic masses
+Mor18m	3D-MoRSE - signal 18 / weighted by atomic masses
+Mor19m	3D-MoRSE - signal 19 / weighted by atomic masses
+Mor20m	3D-MoRSE - signal 20 / weighted by atomic masses
+Mor21m	3D-MoRSE - signal 21 / weighted by atomic masses
+Mor22m	3D-MoRSE - signal 22 / weighted by atomic masses
+Mor23m	3D-MoRSE - signal 23 / weighted by atomic masses
+Mor24m	3D-MoRSE - signal 24 / weighted by atomic masses
+Mor25m	3D-MoRSE - signal 25 / weighted by atomic masses
+Mor26m	3D-MoRSE - signal 26 / weighted by atomic masses
+Mor27m	3D-MoRSE - signal 27 / weighted by atomic masses
+Mor28m	3D-MoRSE - signal 28 / weighted by atomic masses
+Mor29m	3D-MoRSE - signal 29 / weighted by atomic masses
+Mor30m	3D-MoRSE - signal 30 / weighted by atomic masses
+Mor31m	3D-MoRSE - signal 31 / weighted by atomic masses
+Mor32m	3D-MoRSE - signal 32 / weighted by atomic masses
+Mor01v	3D-MoRSE - signal 01 / weighted by atomic van der Waals volumes
+Mor02v	3D-MoRSE - signal 02 / weighted by atomic van der Waals volumes
+Mor03v	3D-MoRSE - signal 03 / weighted by atomic van der Waals volumes
+Mor04v	3D-MoRSE - signal 04 / weighted by atomic van der Waals volumes
+Mor05v	3D-MoRSE - signal 05 / weighted by atomic van der Waals volumes
+Mor06v	3D-MoRSE - signal 06 / weighted by atomic van der Waals volumes
+Mor07v	3D-MoRSE - signal 07 / weighted by atomic van der Waals volumes
+Mor08v	3D-MoRSE - signal 08 / weighted by atomic van der Waals volumes
+Mor09v	3D-MoRSE - signal 09 / weighted by atomic van der Waals volumes
+Mor10v	3D-MoRSE - signal 10 / weighted by atomic van der Waals volumes
+Mor11v	3D-MoRSE - signal 11 / weighted by atomic van der Waals volumes
+Mor12v	3D-MoRSE - signal 12 / weighted by atomic van der Waals volumes
+Mor13v	3D-MoRSE - signal 13 / weighted by atomic van der Waals volumes
+Mor14v	3D-MoRSE - signal 14 / weighted by atomic van der Waals volumes
+Mor15v	3D-MoRSE - signal 15 / weighted by atomic van der Waals volumes
+Mor16v	3D-MoRSE - signal 16 / weighted by atomic van der Waals volumes
+Mor17v	3D-MoRSE - signal 17 / weighted by atomic van der Waals volumes
+Mor18v	3D-MoRSE - signal 18 / weighted by atomic van der Waals volumes
+Mor19v	3D-MoRSE - signal 19 / weighted by atomic van der Waals volumes
+Mor20v	3D-MoRSE - signal 20 / weighted by atomic van der Waals volumes
+Mor21v	3D-MoRSE - signal 21 / weighted by atomic van der Waals volumes
+Mor22v	3D-MoRSE - signal 22 / weighted by atomic van der Waals volumes
+Mor23v	3D-MoRSE - signal 23 / weighted by atomic van der Waals volumes
+Mor24v	3D-MoRSE - signal 24 / weighted by atomic van der Waals volumes
+Mor25v	3D-MoRSE - signal 25 / weighted by atomic van der Waals volumes
+Mor26v	3D-MoRSE - signal 26 / weighted by atomic van der Waals volumes
+Mor27v	3D-MoRSE - signal 27 / weighted by atomic van der Waals volumes
+Mor28v	3D-MoRSE - signal 28 / weighted by atomic van der Waals volumes
+Mor29v	3D-MoRSE - signal 29 / weighted by atomic van der Waals volumes
+Mor30v	3D-MoRSE - signal 30 / weighted by atomic van der Waals volumes
+Mor31v	3D-MoRSE - signal 31 / weighted by atomic van der Waals volumes
+Mor32v	3D-MoRSE - signal 32 / weighted by atomic van der Waals volumes
+Mor01e	3D-MoRSE - signal 01 / weighted by atomic Sanderson electronegativities
+Mor02e	3D-MoRSE - signal 02 / weighted by atomic Sanderson electronegativities
+Mor03e	3D-MoRSE - signal 03 / weighted by atomic Sanderson electronegativities
+Mor04e	3D-MoRSE - signal 04 / weighted by atomic Sanderson electronegativities
+Mor05e	3D-MoRSE - signal 05 / weighted by atomic Sanderson electronegativities
+Mor06e	3D-MoRSE - signal 06 / weighted by atomic Sanderson electronegativities
+Mor07e	3D-MoRSE - signal 07 / weighted by atomic Sanderson electronegativities
+Mor08e	3D-MoRSE - signal 08 / weighted by atomic Sanderson electronegativities
+Mor09e	3D-MoRSE - signal 09 / weighted by atomic Sanderson electronegativities
+Mor10e	3D-MoRSE - signal 10 / weighted by atomic Sanderson electronegativities
+Mor11e	3D-MoRSE - signal 11 / weighted by atomic Sanderson electronegativities
+Mor12e	3D-MoRSE - signal 12 / weighted by atomic Sanderson electronegativities
+Mor13e	3D-MoRSE - signal 13 / weighted by atomic Sanderson electronegativities
+Mor14e	3D-MoRSE - signal 14 / weighted by atomic Sanderson electronegativities
+Mor15e	3D-MoRSE - signal 15 / weighted by atomic Sanderson electronegativities
+Mor16e	3D-MoRSE - signal 16 / weighted by atomic Sanderson electronegativities
+Mor17e	3D-MoRSE - signal 17 / weighted by atomic Sanderson electronegativities
+Mor18e	3D-MoRSE - signal 18 / weighted by atomic Sanderson electronegativities
+Mor19e	3D-MoRSE - signal 19 / weighted by atomic Sanderson electronegativities
+Mor20e	3D-MoRSE - signal 20 / weighted by atomic Sanderson electronegativities
+Mor21e	3D-MoRSE - signal 21 / weighted by atomic Sanderson electronegativities
+Mor22e	3D-MoRSE - signal 22 / weighted by atomic Sanderson electronegativities
+Mor23e	3D-MoRSE - signal 23 / weighted by atomic Sanderson electronegativities
+Mor24e	3D-MoRSE - signal 24 / weighted by atomic Sanderson electronegativities
+Mor25e	3D-MoRSE - signal 25 / weighted by atomic Sanderson electronegativities
+Mor26e	3D-MoRSE - signal 26 / weighted by atomic Sanderson electronegativities
+Mor27e	3D-MoRSE - signal 27 / weighted by atomic Sanderson electronegativities
+Mor28e	3D-MoRSE - signal 28 / weighted by atomic Sanderson electronegativities
+Mor29e	3D-MoRSE - signal 29 / weighted by atomic Sanderson electronegativities
+Mor30e	3D-MoRSE - signal 30 / weighted by atomic Sanderson electronegativities
+Mor31e	3D-MoRSE - signal 31 / weighted by atomic Sanderson electronegativities
+Mor32e	3D-MoRSE - signal 32 / weighted by atomic Sanderson electronegativities
+Mor01p	3D-MoRSE - signal 01 / weighted by atomic polarizabilities
+Mor02p	3D-MoRSE - signal 02 / weighted by atomic polarizabilities
+Mor03p	3D-MoRSE - signal 03 / weighted by atomic polarizabilities
+Mor04p	3D-MoRSE - signal 04 / weighted by atomic polarizabilities
+Mor05p	3D-MoRSE - signal 05 / weighted by atomic polarizabilities
+Mor06p	3D-MoRSE - signal 06 / weighted by atomic polarizabilities
+Mor07p	3D-MoRSE - signal 07 / weighted by atomic polarizabilities
+Mor08p	3D-MoRSE - signal 08 / weighted by atomic polarizabilities
+Mor09p	3D-MoRSE - signal 09 / weighted by atomic polarizabilities
+Mor10p	3D-MoRSE - signal 10 / weighted by atomic polarizabilities
+Mor11p	3D-MoRSE - signal 11 / weighted by atomic polarizabilities
+Mor12p	3D-MoRSE - signal 12 / weighted by atomic polarizabilities
+Mor13p	3D-MoRSE - signal 13 / weighted by atomic polarizabilities
+Mor14p	3D-MoRSE - signal 14 / weighted by atomic polarizabilities
+Mor15p	3D-MoRSE - signal 15 / weighted by atomic polarizabilities
+Mor16p	3D-MoRSE - signal 16 / weighted by atomic polarizabilities
+Mor17p	3D-MoRSE - signal 17 / weighted by atomic polarizabilities
+Mor18p	3D-MoRSE - signal 18 / weighted by atomic polarizabilities
+Mor19p	3D-MoRSE - signal 19 / weighted by atomic polarizabilities
+Mor20p	3D-MoRSE - signal 20 / weighted by atomic polarizabilities
+Mor21p	3D-MoRSE - signal 21 / weighted by atomic polarizabilities
+Mor22p	3D-MoRSE - signal 22 / weighted by atomic polarizabilities
+Mor23p	3D-MoRSE - signal 23 / weighted by atomic polarizabilities
+Mor24p	3D-MoRSE - signal 24 / weighted by atomic polarizabilities
+Mor25p	3D-MoRSE - signal 25 / weighted by atomic polarizabilities
+Mor26p	3D-MoRSE - signal 26 / weighted by atomic polarizabilities
+Mor27p	3D-MoRSE - signal 27 / weighted by atomic polarizabilities
+Mor28p	3D-MoRSE - signal 28 / weighted by atomic polarizabilities
+Mor29p	3D-MoRSE - signal 29 / weighted by atomic polarizabilities
+Mor30p	3D-MoRSE - signal 30 / weighted by atomic polarizabilities
+Mor31p	3D-MoRSE - signal 31 / weighted by atomic polarizabilities
+Mor32p	3D-MoRSE - signal 32 / weighted by atomic polarizabilities
+L1u	1st component size directional WHIM index / unweighted
+L2u	2nd component size directional WHIM index / unweighted
+L3u	3rd component size directional WHIM index / unweighted
+P1u	1st component shape directional WHIM index / unweighted
+P2u	2nd component shape directional WHIM index / unweighted
+G1u	1st component symmetry directional WHIM index / unweighted
+G2u	2st component symmetry directional WHIM index / unweighted
+G3u	3st component symmetry directional WHIM index / unweighted
+E1u	1st component accessibility directional WHIM index / unweighted
+E2u	2nd component accessibility directional WHIM index / unweighted
+E3u	3rd component accessibility directional WHIM index / unweighted
+L1m	1st component size directional WHIM index / weighted by atomic masses
+L2m	2nd component size directional WHIM index / weighted by atomic masses
+L3m	3rd component size directional WHIM index / weighted by atomic masses
+P1m	1st component shape directional WHIM index / weighted by atomic masses
+P2m	2nd component shape directional WHIM index / weighted by atomic masses
+G1m	1st component symmetry directional WHIM index / weighted by atomic masses
+G2m	2st component symmetry directional WHIM index / weighted by atomic masses
+G3m	3st component symmetry directional WHIM index / weighted by atomic masses
+E1m	1st component accessibility directional WHIM index / weighted by atomic masses
+E2m	2nd component accessibility directional WHIM index / weighted by atomic masses
+E3m	3rd component accessibility directional WHIM index / weighted by atomic masses
+L1v	1st component size directional WHIM index / weighted by atomic van der Waals volumes
+L2v	2nd component size directional WHIM index / weighted by atomic van der Waals volumes
+L3v	3rd component size directional WHIM index / weighted by atomic van der Waals volumes
+P1v	1st component shape directional WHIM index / weighted by atomic van der Waals volumes
+P2v	2nd component shape directional WHIM index / weighted by atomic van der Waals volumes
+G1v	1st component symmetry directional WHIM index / weighted by atomic van der Waals volumes
+G2v	2st component symmetry directional WHIM index / weighted by atomic van der Waals volumes
+G3v	3st component symmetry directional WHIM index / weighted by atomic van der Waals volumes
+E1v	1st component accessibility directional WHIM index / weighted by atomic van der Waals volumes
+E2v	2nd component accessibility directional WHIM index / weighted by atomic van der Waals volumes
+E3v	3rd component accessibility directional WHIM index / weighted by atomic van der Waals volumes
+L1e	1st component size directional WHIM index / weighted by atomic Sanderson electronegativities
+L2e	2nd component size directional WHIM index / weighted by atomic Sanderson electronegativities
+L3e	3rd component size directional WHIM index / weighted by atomic Sanderson electronegativities
+P1e	1st component shape directional WHIM index / weighted by atomic Sanderson electronegativities
+P2e	2nd component shape directional WHIM index / weighted by atomic Sanderson electronegativities
+G1e	1st component symmetry directional WHIM index / weighted by atomic Sanderson electronegativities
+G2e	2st component symmetry directional WHIM index / weighted by atomic Sanderson electronegativities
+G3e	3st component symmetry directional WHIM index / weighted by atomic Sanderson electronegativities
+E1e	1st component accessibility directional WHIM index / weighted by atomic Sanderson electronegativities
+E2e	2nd component accessibility directional WHIM index / weighted by atomic Sanderson electronegativities
+E3e	3rd component accessibility directional WHIM index / weighted by atomic Sanderson electronegativities
+L1p	1st component size directional WHIM index / weighted by atomic polarizabilities
+L2p	2nd component size directional WHIM index / weighted by atomic polarizabilities
+L3p	3rd component size directional WHIM index / weighted by atomic polarizabilities
+P1p	1st component shape directional WHIM index / weighted by atomic polarizabilities
+P2p	2nd component shape directional WHIM index / weighted by atomic polarizabilities
+G1p	1st component symmetry directional WHIM index / weighted by atomic polarizabilities
+G2p	2st component symmetry directional WHIM index / weighted by atomic polarizabilities
+G3p	3st component symmetry directional WHIM index / weighted by atomic polarizabilities
+E1p	1st component accessibility directional WHIM index / weighted by atomic polarizabilities
+E2p	2nd component accessibility directional WHIM index / weighted by atomic polarizabilities
+E3p	3rd component accessibility directional WHIM index / weighted by atomic polarizabilities
+L1s	1st component size directional WHIM index / weighted by atomic electrotopological states
+L2s	2nd component size directional WHIM index / weighted by atomic electrotopological states
+L3s	3rd component size directional WHIM index / weighted by atomic electrotopological states
+P1s	1st component shape directional WHIM index / weighted by atomic electrotopological states
+P2s	2nd component shape directional WHIM index / weighted by atomic electrotopological states
+G1s	1st component symmetry directional WHIM index / weighted by atomic electrotopological states
+G2s	2st component symmetry directional WHIM index / weighted by atomic electrotopological states
+G3s	3st component symmetry directional WHIM index / weighted by atomic electrotopological states
+E1s	1st component accessibility directional WHIM index / weighted by atomic electrotopological states
+E2s	2nd component accessibility directional WHIM index / weighted by atomic electrotopological states
+E3s	3rd component accessibility directional WHIM index / weighted by atomic electrotopological states
+Tu	T total size index / unweighted
+Tm	T total size index / weighted by atomic masses
+Tv	T total size index / weighted by atomic van der Waals volumes
+Te	T total size index / weighted by atomic Sanderson electronegativities
+Tp	T total size index / weighted by atomic polarizabilities
+Ts	T total size index / weighted by atomic electrotopological states
+Au	A total size index / unweighted
+Am	A total size index / weighted by atomic masses
+Av	A total size index / weighted by atomic van der Waals volumes
+Ae	A total size index / weighted by atomic Sanderson electronegativities
+Ap	A total size index / weighted by atomic polarizabilities
+As	A total size index / weighted by atomic electrotopological states
+Gu	G total symmetry index / unweighted
+Gm	G total symmetry index / weighted by atomic masses
+Gs	G total symmetry index / weighted by atomic electrotopological states
+Ku	K global shape index / unweighted
+Km	K global shape index / weighted by atomic masses
+Kv	K global shape index / weighted by atomic van der Waals volumes
+Ke	K global shape index / weighted by atomic Sanderson electronegativities
+Kp	K global shape index / weighted by atomic polarizabilities
+Ks	K global shape index / weighted by atomic electrotopological states
+Du	D total accessibility index / unweighted
+Dm	D total accessibility index / weighted by atomic masses
+Dv	D total accessibility index / weighted by atomic van der Waals volumes
+De	D total accessibility index / weighted by atomic Sanderson electronegativities
+Dp	D total accessibility index / weighted by atomic polarizabilities
+Ds	D total accessibility index / weighted by atomic electrotopological states
+Vu	V total size index / unweighted
+Vm	V total size index / weighted by atomic masses
+Vv	V total size index / weighted by atomic van der Waals volumes
+Ve	V total size index / weighted by atomic Sanderson electronegativities
+Vp	V total size index / weighted by atomic polarizabilities
+Vs	V total size index / weighted by atomic electrotopological states
+ITH	total information content on the leverage equality
+ISH	standardized information content on the leverage equality
+HIC	mean information content on the leverage magnitude
+HGM	geometric mean on the leverage magnitude
+H0u	H autocorrelation of lag 0 / unweighted
+H1u	H autocorrelation of lag 1 / unweighted
+H2u	H autocorrelation of lag 2 / unweighted
+H3u	H autocorrelation of lag 3 / unweighted
+H4u	H autocorrelation of lag 4 / unweighted
+H5u	H autocorrelation of lag 5 / unweighted
+H6u	H autocorrelation of lag 6 / unweighted
+H7u	H autocorrelation of lag 7 / unweighted
+H8u	H autocorrelation of lag 8 / unweighted
+HTu	H total index / unweighted
+HATS0u	leverage-weighted autocorrelation of lag 0 / unweighted
+HATS1u	leverage-weighted autocorrelation of lag 1 / unweighted
+HATS2u	leverage-weighted autocorrelation of lag 2 / unweighted
+HATS3u	leverage-weighted autocorrelation of lag 3 / unweighted
+HATS4u	leverage-weighted autocorrelation of lag 4 / unweighted
+HATS5u	leverage-weighted autocorrelation of lag 5 / unweighted
+HATS6u	leverage-weighted autocorrelation of lag 6 / unweighted
+HATS7u	leverage-weighted autocorrelation of lag 7 / unweighted
+HATS8u	leverage-weighted autocorrelation of lag 8 / unweighted
+HATSu	leverage-weighted total index / unweighted
+H0m	H autocorrelation of lag 0 / weighted by atomic masses
+H1m	H autocorrelation of lag 1 / weighted by atomic masses
+H2m	H autocorrelation of lag 2 / weighted by atomic masses
+H3m	H autocorrelation of lag 3 / weighted by atomic masses
+H4m	H autocorrelation of lag 4 / weighted by atomic masses
+H5m	H autocorrelation of lag 5 / weighted by atomic masses
+H6m	H autocorrelation of lag 6 / weighted by atomic masses
+H7m	H autocorrelation of lag 7 / weighted by atomic masses
+H8m	H autocorrelation of lag 8 / weighted by atomic masses
+HTm	H total index / weighted by atomic masses
+HATS0m	leverage-weighted autocorrelation of lag 0 / weighted by atomic masses
+HATS1m	leverage-weighted autocorrelation of lag 1 / weighted by atomic masses
+HATS2m	leverage-weighted autocorrelation of lag 2 / weighted by atomic masses
+HATS3m	leverage-weighted autocorrelation of lag 3 / weighted by atomic masses
+HATS4m	leverage-weighted autocorrelation of lag 4 / weighted by atomic masses
+HATS5m	leverage-weighted autocorrelation of lag 5 / weighted by atomic masses
+HATS6m	leverage-weighted autocorrelation of lag 6 / weighted by atomic masses
+HATS7m	leverage-weighted autocorrelation of lag 7 / weighted by atomic masses
+HATS8m	leverage-weighted autocorrelation of lag 8 / weighted by atomic masses
+HATSm	leverage-weighted total index / weighted by atomic masses
+H0v	H autocorrelation of lag 0 / weighted by atomic van der Waals volumes
+H1v	H autocorrelation of lag 1 / weighted by atomic van der Waals volumes
+H2v	H autocorrelation of lag 2 / weighted by atomic van der Waals volumes
+H3v	H autocorrelation of lag 3 / weighted by atomic van der Waals volumes
+H4v	H autocorrelation of lag 4 / weighted by atomic van der Waals volumes
+H5v	H autocorrelation of lag 5 / weighted by atomic van der Waals volumes
+H6v	H autocorrelation of lag 6 / weighted by atomic van der Waals volumes
+H7v	H autocorrelation of lag 7 / weighted by atomic van der Waals volumes
+H8v	H autocorrelation of lag 8 / weighted by atomic van der Waals volumes
+HTv	H total index / weighted by atomic van der Waals volumes
+HATS0v	leverage-weighted autocorrelation of lag 0 / weighted by atomic van der Waals volumes
+HATS1v	leverage-weighted autocorrelation of lag 1 / weighted by atomic van der Waals volumes
+HATS2v	leverage-weighted autocorrelation of lag 2 / weighted by atomic van der Waals volumes
+HATS3v	leverage-weighted autocorrelation of lag 3 / weighted by atomic van der Waals volumes
+HATS4v	leverage-weighted autocorrelation of lag 4 / weighted by atomic van der Waals volumes
+HATS5v	leverage-weighted autocorrelation of lag 5 / weighted by atomic van der Waals volumes
+HATS6v	leverage-weighted autocorrelation of lag 6 / weighted by atomic van der Waals volumes
+HATS7v	leverage-weighted autocorrelation of lag 7 / weighted by atomic van der Waals volumes
+HATS8v	leverage-weighted autocorrelation of lag 8 / weighted by atomic van der Waals volumes
+HATSv	leverage-weighted total index / weighted by atomic van der Waals volumes
+H0e	H autocorrelation of lag 0 / weighted by atomic Sanderson electronegativities
+H1e	H autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities
+H2e	H autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities
+H3e	H autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities
+H4e	H autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities
+H5e	H autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities
+H6e	H autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities
+H7e	H autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities
+H8e	H autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities
+HTe	H total index / weighted by atomic Sanderson electronegativities
+HATS0e	leverage-weighted autocorrelation of lag 0 / weighted by atomic Sanderson electronegativities
+HATS1e	leverage-weighted autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities
+HATS2e	leverage-weighted autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities
+HATS3e	leverage-weighted autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities
+HATS4e	leverage-weighted autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities
+HATS5e	leverage-weighted autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities
+HATS6e	leverage-weighted autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities
+HATS7e	leverage-weighted autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities
+HATS8e	leverage-weighted autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities
+HATSe	leverage-weighted total index / weighted by atomic Sanderson electronegativities
+H0p	H autocorrelation of lag 0 / weighted by atomic polarizabilities
+H1p	H autocorrelation of lag 1 / weighted by atomic polarizabilities
+H2p	H autocorrelation of lag 2 / weighted by atomic polarizabilities
+H3p	H autocorrelation of lag 3 / weighted by atomic polarizabilities
+H4p	H autocorrelation of lag 4 / weighted by atomic polarizabilities
+H5p	H autocorrelation of lag 5 / weighted by atomic polarizabilities
+H6p	H autocorrelation of lag 6 / weighted by atomic polarizabilities
+H7p	H autocorrelation of lag 7 / weighted by atomic polarizabilities
+H8p	H autocorrelation of lag 8 / weighted by atomic polarizabilities
+HTp	H total index / weighted by atomic polarizabilities
+HATS0p	leverage-weighted autocorrelation of lag 0 / weighted by atomic polarizabilities
+HATS1p	leverage-weighted autocorrelation of lag 1 / weighted by atomic polarizabilities
+HATS2p	leverage-weighted autocorrelation of lag 2 / weighted by atomic polarizabilities
+HATS3p	leverage-weighted autocorrelation of lag 3 / weighted by atomic polarizabilities
+HATS4p	leverage-weighted autocorrelation of lag 4 / weighted by atomic polarizabilities
+HATS5p	leverage-weighted autocorrelation of lag 5 / weighted by atomic polarizabilities
+HATS6p	leverage-weighted autocorrelation of lag 6 / weighted by atomic polarizabilities
+HATS7p	leverage-weighted autocorrelation of lag 7 / weighted by atomic polarizabilities
+HATS8p	leverage-weighted autocorrelation of lag 8 / weighted by atomic polarizabilities
+HATSp	leverage-weighted total index / weighted by atomic polarizabilities
+RCON	Randic-type R matrix connectivity
+RARS	R matrix average row sum
+REIG	first eigenvalue of the R matrix
+R1u	R autocorrelation of lag 1 / unweighted
+R2u	R autocorrelation of lag 2 / unweighted
+R3u	R autocorrelation of lag 3 / unweighted
+R4u	R autocorrelation of lag 4 / unweighted
+R5u	R autocorrelation of lag 5 / unweighted
+R6u	R autocorrelation of lag 6 / unweighted
+R7u	R autocorrelation of lag 7 / unweighted
+R8u	R autocorrelation of lag 8 / unweighted
+RTu	R total index / unweighted
+R1u+	R maximal autocorrelation of lag 1 / unweighted
+R2u+	R maximal autocorrelation of lag 2 / unweighted
+R3u+	R maximal autocorrelation of lag 3 / unweighted
+R4u+	R maximal autocorrelation of lag 4 / unweighted
+R5u+	R maximal autocorrelation of lag 5 / unweighted
+R6u+	R maximal autocorrelation of lag 6 / unweighted
+R7u+	R maximal autocorrelation of lag 7 / unweighted
+R8u+	R maximal autocorrelation of lag 8 / unweighted
+RTu+	R maximal index / unweighted
+R1m	R autocorrelation of lag 1 / weighted by atomic masses
+R2m	R autocorrelation of lag 2 / weighted by atomic masses
+R3m	R autocorrelation of lag 3 / weighted by atomic masses
+R4m	R autocorrelation of lag 4 / weighted by atomic masses
+R5m	R autocorrelation of lag 5 / weighted by atomic masses
+R6m	R autocorrelation of lag 6 / weighted by atomic masses
+R7m	R autocorrelation of lag 7 / weighted by atomic masses
+R8m	R autocorrelation of lag 8 / weighted by atomic masses
+RTm	R total index / weighted by atomic masses
+R1m+	R maximal autocorrelation of lag 1 / weighted by atomic masses
+R2m+	R maximal autocorrelation of lag 2 / weighted by atomic masses
+R3m+	R maximal autocorrelation of lag 3 / weighted by atomic masses
+R4m+	R maximal autocorrelation of lag 4 / weighted by atomic masses
+R5m+	R maximal autocorrelation of lag 5 / weighted by atomic masses
+R6m+	R maximal autocorrelation of lag 6 / weighted by atomic masses
+R7m+	R maximal autocorrelation of lag 7 / weighted by atomic masses
+R8m+	R maximal autocorrelation of lag 8 / weighted by atomic masses
+RTm+	R maximal index / weighted by atomic masses
+R1v	R autocorrelation of lag 1 / weighted by atomic van der Waals volumes
+R2v	R autocorrelation of lag 2 / weighted by atomic van der Waals volumes
+R3v	R autocorrelation of lag 3 / weighted by atomic van der Waals volumes
+R4v	R autocorrelation of lag 4 / weighted by atomic van der Waals volumes
+R5v	R autocorrelation of lag 5 / weighted by atomic van der Waals volumes
+R6v	R autocorrelation of lag 6 / weighted by atomic van der Waals volumes
+R7v	R autocorrelation of lag 7 / weighted by atomic van der Waals volumes
+R8v	R autocorrelation of lag 8 / weighted by atomic van der Waals volumes
+RTv	R total index / weighted by atomic van der Waals volumes
+R1v+	R maximal autocorrelation of lag 1 / weighted by atomic van der Waals volumes
+R2v+	R maximal autocorrelation of lag 2 / weighted by atomic van der Waals volumes
+R3v+	R maximal autocorrelation of lag 3 / weighted by atomic van der Waals volumes
+R4v+	R maximal autocorrelation of lag 4 / weighted by atomic van der Waals volumes
+R5v+	R maximal autocorrelation of lag 5 / weighted by atomic van der Waals volumes
+R6v+	R maximal autocorrelation of lag 6 / weighted by atomic van der Waals volumes
+R7v+	R maximal autocorrelation of lag 7 / weighted by atomic van der Waals volumes
+R8v+	R maximal autocorrelation of lag 8 / weighted by atomic van der Waals volumes
+RTv+	R maximal index / weighted by atomic van der Waals volumes
+R1e	R autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities
+R2e	R autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities
+R3e	R autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities
+R4e	R autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities
+R5e	R autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities
+R6e	R autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities
+R7e	R autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities
+R8e	R autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities
+RTe	R total index / weighted by atomic Sanderson electronegativities
+R1e+	R maximal autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities
+R2e+	R maximal autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities
+R3e+	R maximal autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities
+R4e+	R maximal autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities
+R5e+	R maximal autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities
+R6e+	R maximal autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities
+R7e+	R maximal autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities
+R8e+	R maximal autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities
+RTe+	R maximal index / weighted by atomic Sanderson electronegativities
+R1p	R autocorrelation of lag 1 / weighted by atomic polarizabilities
+R2p	R autocorrelation of lag 2 / weighted by atomic polarizabilities
+R3p	R autocorrelation of lag 3 / weighted by atomic polarizabilities
+R4p	R autocorrelation of lag 4 / weighted by atomic polarizabilities
+R5p	R autocorrelation of lag 5 / weighted by atomic polarizabilities
+R6p	R autocorrelation of lag 6 / weighted by atomic polarizabilities
+R7p	R autocorrelation of lag 7 / weighted by atomic polarizabilities
+R8p	R autocorrelation of lag 8 / weighted by atomic polarizabilities
+RTp	R total index / weighted by atomic polarizabilities
+R1p+	R maximal autocorrelation of lag 1 / weighted by atomic polarizabilities
+R2p+	R maximal autocorrelation of lag 2 / weighted by atomic polarizabilities
+R3p+	R maximal autocorrelation of lag 3 / weighted by atomic polarizabilities
+R4p+	R maximal autocorrelation of lag 4 / weighted by atomic polarizabilities
+R5p+	R maximal autocorrelation of lag 5 / weighted by atomic polarizabilities
+R6p+	R maximal autocorrelation of lag 6 / weighted by atomic polarizabilities
+R7p+	R maximal autocorrelation of lag 7 / weighted by atomic polarizabilities
+R8p+	R maximal autocorrelation of lag 8 / weighted by atomic polarizabilities
+RTp+	R maximal index / weighted by atomic polarizabilities
+nCp	number of terminal primary C(sp3) Y = any terminal atom or heteroaromatic group (i.e. H, X, OH, NH2, etc.)
+nCs	number of total secondary C(sp3) Y = H or any heteroatom
+nCt	number of total tertiary C(sp3) Y = H or any heteroatom
+nCq	number of total quaternary C(sp3)
+nCrs	number of ring secondary C(sp3) Y = H or any heteroatom
+nCrt	number of ring tertiary C(sp3) Y = H or any heteroatom
+nCrq	number of ring quaternary C(sp3)
+nCar	number of aromatic C(sp2)
+nCbH	number of unsubstituted benzene C(sp2)
+nCb–	number of substituted benzene C(sp2) Y = carbon or any heteroatom
+nCconj	number of non-aromatic conjugated C(sp2)
+nR=Cp	number of terminal primary C(sp2) Y = any terminal atom or heteroaromatic group (i.e. H, X, OH, NH2, etc.)
+nR=Cs	number of aliphatic secondary C(sp2) Y = H or any heteroatom
+nR=Ct	number of aliphatic tertiary C(sp2)
+n=C=	number of allenes groups
+nR#CH/X	number of terminal C(sp) Y = any terminal atom or heteroaromatic group (i.e. H, X, OH, NH2, etc.)
+nR#C–	number of non-terminal C(sp) Y = C or any non-terminal heteroatom
+nROCN	number of cyanates (aliphatic)
+nArOCN	number of cyanates (aromatic)
+nRNCO	number of isocyanates (aliphatic)
+nArNCO	number of isocyanates (aromatic)
+nRSCN	number of thiocyanates (aliphatic)
+nArSCN	number of thiocyanates (aromatic)
+nRNCS	number of isothiocyanates (aliphatic)
+nArNCS	number of isothiocyanates (aromatic)
+nRCOOH	number of carboxylic acids (aliphatic)
+nArCOOH	number of carboxylic acids (aromatic)
+nRCOOR	number of esters (aliphatic) Y = Ar or Al (not H)                                  Al = H or aliphatic group linked through C
+nArCOOR	number of esters (aromatic) Y = Al or Ar
+nRCONH2	number of primary amides (aliphatic) Al = H or aliphatic group linked through C
+nArCONH2	number of primary amides (aromatic)
+nRCONHR	number of secondary amides (aliphatic)   Y = Ar or Al (not H, not C = O) Al = H or aliphatic group linked through C
+nArCONHR	number of secondary amides (aromatic) Y = Ar or Al (not H, not C = O)
+nRCONR2	number of tertiary amides (aliphatic)  Y = Ar or Al (not H, not C = O) Al = H or aliphatic group linked through C
+nArCONR2	number of tertiary amides (aromatic) Y = Ar or Al (not H, not C = O)
+nROCON	number of (thio-) carbamates (aliphatic) Y = O or S Al = H or aliphatic group linked through any atom
+nArOCON	number of (thio-) carbamates (aromatic) Y1 = O or S Y2 = H or aliphatic or aromatic group linked through any atom Ar = aromatic group linked through any atom
+nRCOX	number of acyl halogenides (aliphatic)
+nArCOX	number of acyl halogenides (aromatic)
+nRCSOH	number of thioacids (aliphatic)
+nArCSOH	number of thioacids (aromatic)
+nRCSSH	number of dithioacids (aliphatic)
+nArCSSH	number of dithioacids (aromatic)
+nRCOSR	number of thioesters (aliphatic) Y = Ar or Al (not H) Al = H or aliphatic group linked through C
+nArCOSR	number of thioesters (aromatic)
+nRCSSR	number of dithioesters (aliphatic) Y = Ar or Al (not H) Al = H or aliphatic group linked through C
+nArCSSR	number of dithioesters (aromatic) Y = Ar or Al (not H)
+nRCHO	number of aldehydes (aliphatic)
+nArCHO	number of aldehydes (aromatic)
+nRCO	number of ketones (aliphatic)
+nArCO	number of ketones (aromatic) Y = Al or Ar
+nCONN	number of urea (-thio) derivatives Y = O or S
+nC=O(OR)2	number of carbonate (-thio) derivatives Y = O or S
+nN=C-N<	number of amidine derivatives Y = C or H
+nC(=N)N2	number of guanidine derivatives
+nRC=N	number of imines (aliphatic)  Y = H,C or N (two-connected) Al = H or aliphatic group linked through C
+nArC=N	number of imines (aromatic) Y = H,C or N (two-connected)
+nRCNO	number of oximes (aliphatic) Y = H, Ar or Al
+nArCNO	number of oximes (aromatic) Y = H, Ar or Al
+nRNH2	number of primary amines (aliphatic) Al = aliphatic group linked through C  (not C = O)
+nArNH2	number of primary amines (aromatic)
+nRNHR	number of secondary amines (aliphatic) Al = aliphatic group linked through C  (not C = O)
+nArNHR	number of secondary amines (aromatic) Y = Ar or Al (not C = O)
+nRNR2	number of tertiary amines (aliphatic) Al = aliphatic group linked through C  (not C = O)
+nArNR2	number of tertiary amines (aromatic) Y = Ar or Al (not C = O)
+nN-N	number of N hydrazines Y = C or H
+nN=N	number of N azo-derivatives Y = C or H
+nRCN	number of nitriles (aliphatic)
+nArCN	number of nitriles (aromatic)
+nN+	number of positive charged N
+nNq	number of quaternary N
+nRNHO	number of hydroxylamines (aliphatic) Y = H, Al or Ar
+nArNHO	number of hydroxylamines (aromatic) Y = H, Al or Ar
+nRNNOx	number of N-nitroso groups (aliphatic) Al = H or aliphatic group linked through C
+nArNNOx	number of N-nitroso groups (aromatic) Y = H, Al or Ar
+nRNO	number of nitroso groups (aliphatic)
+nArNO	number of nitroso groups (aromatic)
+nRNO2	number of nitro groups (aliphatic) Al = H or aliphatic group linked through carbon
+nArNO2	number of nitro groups (aromatic) Al = aromatic group linked through carbon
+nN(CO)2	number of imides (thio-) Y = H or C                 Y1 = O or S
+nC=N-N<	number of hydrazones Y = C or H
+nROH	number of hydroxyl groups Al = aliphatic group linked through any atom
+nArOH	number of aromatic hydroxyls Ar = aromatic group linked through any atom
+nOHp	number of primary alcohols
+nOHs	number of secondary alcohols
+nOHt	number of tertiary alcohols
+nROR	number of ethers (aliphatic) Al = aliphatic group linked through C (not C = O, not C # N)
+nArOR	number of ethers (aromatic) Y = Ar or Al (not C = O, not C # N)
+nROX	number of hypohalogenides (aliphatic)
+nArOX	number of hypohalogenides (aromatic)
+nO(C=O)2	number of anhydrides (thio-) Y = O or S
+nH2O	number of water molecules
+nSH	number of thiols
+nC=S	number of thioketones
+nRSR	number of sulfides
+nRSSR	number of disulfides
+nSO	number of sulfoxides
+nS(=O)2	number of sulfones
+nSOH	number of sulfenic (thio-) acids Y = O or S
+nSOOH	number of sulfinic (thio-/dithio-)acids Y = O or S
+nSO2OH	number of sulfonic (thio-/dithio-) acids Y = O or S
+nSO3OH	number of sulfuric (thio-/dithio-) acids Y = O or S
+nSO2	number of sulfites (thio-/ dithio-) Y = O or S
+nSO3	number of sulfonates (thio- / dithio-) Y = O or S
+nSO4	number of sulfates (thio- / dithio-) Y = O or S
+nSO2N	number of sulfonamides / sulfinamides / sulfenamides (thio- / dithio-)
+nPO3	number of phosphites / thiophosphites Y = O or S
+nPO4	number of phosphates / thiophosphates Y = O or S
+nPR3	number of phosphanes Y = H, C, halogens
+nP(=O)O2R	number of phosphonates / thiophosphonates Y = O or S Y1 = H, C, halogens
+nP(=O)R3/nPR5	number of phosphoranes / thiophosphoranes Y = O or S
+nCH2RX	number of CH2RX
+nCHR2X	number of CHR2X
+nCR3X	number of CR3X
+nR=CHX	number of R=CHX
+nR=CRX	number of R=CRX
+nR#CX	number of R#CX
+nCHRX2	number of CHRX2
+nCR2X2	number of CR2X2
+nR=CX2	number of R=CX2
+nCRX3	number of CRX3
+nArX	number of X on aromatic ring
+nCXr	number of X on ring C(sp3)
+nCXr=	number of X on ring C(sp2)
+nCconjX	number of X on exo-conjugated C
+nAziridines	number of Aziridines
+nOxiranes	number of Oxiranes
+nThiranes	number of Thiranes
+nAzetidines	number of Azetidines
+nOxetanes	number of Oxetanes
+nThioethanes	number of Thioethanes
+nBeta-Lactams	number of Beta-Lactams
+nPyrrolidines	number of Pyrrolidines
+nOxolanes	number of Oxolanes
+nth-Thiophenes	number of tetrahydro-Thiophenes
+nPyrroles	number of Pyrroles
+nPyrazoles	number of Pyrazoles
+nImidazoles	number of Imidazoles
+nFuranes	number of Furanes
+nThiophenes	number of Thiophenes
+nOxazoles	number of Oxazoles
+nIsoxazoles	number of Isoxazoles
+nThiazoles	number of Thiazoles
+nIsothiazoles	number of Isothiazoles
+nTriazoles	number of Triazoles
+nPyridines	number of Pyridines
+nPyridazines	number of Pyridazines
+nPyrimidines	number of Pyrimidines
+nPyrazines	number of Pyrazines
+n135-Triazines	number of 135-Triazines
+n124-Triazines	number of 124-Triazines
+nHDon	number of donor atoms for H-bonds (N and O)
+nHAcc	number of acceptor atoms for H-bonds (N, O, F)
+nHBonds	number of intramolecular H-bonds Y1 = B, N, O, Al, P, S Y2 = N, O, F The geometric distance between H and Y2 must be in the range 1 - 2,7 A.
+C-001	CH3R / CH4
+C-002	CH2R2
+C-003	CHR3
+C-004	CR4
+C-005	CH3X
+C-006	CH2RX
+C-007	CH2X2
+C-008	CHR2X
+C-009	CHRX2
+C-010	CHX3
+C-011	CR3X
+C-012	CR2X2
+C-013	CRX3
+C-014	CX4
+C-015	=CH2
+C-016	=CHR
+C-017	=CR2
+C-018	=CHX
+C-019	=CRX
+C-020	=CX2
+C-021	#CH
+C-022	#CR / R=C=R
+C-023	#CX
+C-024	R--CH--R
+C-025	R--CR--R
+C-026	R--CX--R
+C-027	R--CH--X
+C-028	R--CR--X
+C-029	R--CX--X
+C-030	X--CH--X
+C-031	X--CR--X
+C-032	X--CX--X
+C-033	R--CH..X
+C-034	R--CR..X
+C-035	R--CX..X
+C-036	Al-CH=X
+C-037	Ar-CH=X
+C-038	Al-C(=X)-Al
+C-039	Ar-C(=X)-R
+C-040	R-C(=X)-X / R-C#X / X=C=X
+C-041	X-C(=X)-X
+C-042	X--CH..X
+C-043	X--CR..X
+C-044	X--CX..X
+U-045	undefined
+H-046	Ha attached to C0(sp3) no X attached to next C
+H-047	Ha attached to C1(sp3) / C0(sp2)
+H-048	Ha attached to C2(sp3) / C1(sp2) / C0(sp)
+H-049	Ha attached to C3(sp3) / C2(sp2) / C3(sp2) / C3(sp)
+H-050	H attached to heteroatom
+H-051	H attached to alpha-Cb
+H-052	Ha attached to C0(sp3) with 1X attached to next C
+H-053	Ha attached to C0(sp3) with 2X attached to next C
+H-054	Ha attached to C0(sp3) with 3X attached to next C
+H-055	Ha attached to C0(sp3) with 4X attached to next C
+O-056	alcohol
+O-057	phenol / enol / carboxyl OH
+O-058	=O
+O-059	Al-O-Al
+O-060	Al-O-Ar / Ar-O-Ar / R..O..R / R-O-C=X
+O-061	O-- c
+O-062	O- (negatively charged)
+O-063	R-O-O-R
+Se-064	Any-Se-Any
+Se-065	=Se
+N-066	Al-NH2
+N-067	Al2-NH
+N-068	Al3-N
+N-069	Ar-NH2 / X-NH2
+N-070	Ar-NH-Al
+N-071	Ar-NAl2
+N-072	RCO-N< / >N-X=X
+N-073	Ar2NH / Ar3N / Ar2N-Al / R..N..Rd
+N-074	R#N / R=N-
+N-075	R--N--Re / R--N--X
+N-076	Ar-NO2 / R--N(--R)--Of / RO-NO
+N-077	Al-NO2
+N-078	Ar-N=X / X-N=X
+N-079	N+ (positively charged)
+U-080	undefined
+F-081	Fa attached to C1(sp3)
+F-082	Fa attached to C2(sp3)
+F-083	Fa attached to C3(sp3)
+F-084	Fa attached to C1(sp2)
+F-085	Fa attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X
+Cl-086	Cla attached to C1(sp3)
+Cl-087	Cla attached to C2(sp3)
+Cl-088	Cla attached to C3(sp3)
+Cl-089	Cla attached to C1(sp2)
+Cl-090	Cla attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X
+Br-091	Bra attached to C1(sp3)
+Br-092	Bra attached to C2(sp3)
+Br-093	Bra attached to C3(sp3)
+Br-094	Bra attached to C1(sp2)
+Br-095	Bra attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X
+I-096	Ia attached to C1(sp3)
+I-097	Ia attached to C2(sp3)
+I-098	Ia attached to C3(sp3)
+I-099	Ia attached to C1(sp2)
+I-100	Ia attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X
+F-101	fluoride ion
+Cl-102	chloride ion
+Br-103	bromide ion
+I-104	iodide ion
+U-105	undefined
+S-106	R-SH
+S-107	R2S / RS-SR
+S-108	R=S
+S-109	R-SO-R
+S-110	R-SO2-R
+Si-111	>Si<
+B-112	>B- as in boranes
+U-113	undefined
+U-114	undefined
+P-115	P ylids
+P-116	R3-P=X
+P-117	X3-P=X (phosphate)
+P-118	PX3 (phosphite)
+P-119	PR3 (phosphine)
+P-120	C-P(X)2=X (phosphonate)
+qpmax	maximum positive charge
+qnmax	maximum negative charge
+Qpos	total positive charge
+Qneg	total negative charge
+Qtot	total absolute charge (electronic charge index - ECI)
+Qmean	mean absolute charge (charge polarization)
+Q2	total squared charge
+RPCG	relative positive charge
+RNCG	relative negative charge
+SPP	submolecular polarity parameter
+TE1	topological electronic descriptor
+TE2	topological electronic descriptor (bond resctricted)
+PCWTe	partial charge weighted topological electronic descriptor
+LDI	local dipole index
+Ui	unsaturation index
+Hy	hydrophilic factor
+AMR	molar refractivity
+TPSA(NO)	topological polar surface area using N, O polar contributions
+TPSA(tot)	topological polar surface area using N, O, S, P polar contributions
+MLogP	Moriguchi octanol-water partition coefficient
+MLOGP2	Squared Moriguchi octanol-water partition coeff. (logP^2)
+ALOGP	Ghose-Crippen octanol-water partition coeff. (logP)
+ALOGP2	Squared Ghose-Crippen octanol-water partition coeff. (logP^2)
+LAI	Lipinski alert index
+GVWAI-80	Ghose-Viswanadhan-Wendoloski drug-like index at 80%
+GVWAI-50	Ghose-Viswanadhan-Wendoloski drug-like index at 50%
+Inflammat-80	Ghose-Viswanadhan-Wendoloski antiinflammatory-like index at 80%
+Inflammat-50	Ghose-Viswanadhan-Wendoloski antiinflammatory-like index at 50%
+Depressant-80	Ghose-Viswanadhan-Wendoloski antidepressant-like index at 80%
+Depressant-50	Ghose-Viswanadhan-Wendoloski antidepressant-like index at 50%
+Psychotic-80	Ghose-Viswanadhan-Wendoloski antipsychotic-like index at 80%
+Psychotic-50	Ghose-Viswanadhan-Wendoloski antipsychotic-like index at 50%
+Hypertens-80	Ghose-Viswanadhan-Wendoloski antihypertensive-like index at 80%
+Hypertens-50	Ghose-Viswanadhan-Wendoloski antihypertensive-like index at 50%
+Hypnotic-80	Ghose-Viswanadhan-Wendoloski hypnotic-like index at 80%
+Hypnotic-50	Ghose-Viswanadhan-Wendoloski hypnotic-like index at 50%
+Neoplastic-80	Ghose-Viswanadhan-Wendoloski antineoplastic-like index at 80%
+Neoplastic-50	Ghose-Viswanadhan-Wendoloski antineoplastic-like index at 50%
+Infective-80	Ghose-Viswanadhan-Wendoloski antiinfective-like index at 80%
+Infective-50	Ghose-Viswanadhan-Wendoloski antiinfective-like index at 50%
+BLTF96	Verhaar model of Fish base-line toxicity for Fish (96h) from MLOGP (mmol/l)
+BLTD48	Verhaar model of Daphnia base-line toxicity  for Daphnia (48h) from MLOGP (mmol/l)
+BLTA96	Verhaar model of Algae base-line toxicity for Algae (96h) from MLOGP (mmol/l)
+B01[C-C]	presence/absence of C-C at topological distance 1
+B01[C-N]	presence/absence of C-N at topological distance 1
+B01[C-O]	presence/absence of C-O at topological distance 1
+B01[C-S]	presence/absence of C-S at topological distance 1
+B01[C-P]	presence/absence of C-P at topological distance 1
+B01[C-F]	presence/absence of C-F at topological distance 1
+B01[C-Cl]	presence/absence of C-Cl at topological distance 1
+B01[C-Br]	presence/absence of C-Br at topological distance 1
+B01[C-I]	presence/absence of C-I at topological distance 1
+B01[C-B]	presence/absence of C-B at topological distance 1
+B01[C-Si]	presence/absence of C-Si at topological distance 1
+B01[C-X]	presence/absence of C-X at topological distance 1
+B01[N-N]	presence/absence of N-N at topological distance 1
+B01[N-O]	presence/absence of N-O at topological distance 1
+.........	..........................................................
+B10[Si-X]	presence/absence of Si-X at topological distance 10
+B10[X-X]	presence/absence of X-X at topological distance 10
+F01[C-C]	frequency of C-C at topological distance 1
+F01[C-N]	frequency of C-N at topological distance 1
+F01[C-O]	frequency of C-O at topological distance 1
+F01[C-S]	frequency of C-S at topological distance 1
+F01[C-P]	frequency of C-P at topological distance 1
+F01[C-F]	frequency of C-F at topological distance 1
+F01[C-Cl]	frequency of C-Cl at topological distance 1
+F01[C-Br]	frequency of C-Br at topological distance 1
+F01[C-I]	frequency of C-I at topological distance 1
+F01[C-B]	frequency of C-B at topological distance 1
+F01[C-Si]	frequency of C-Si at topological distance 1
+F01[C-X]	frequency of C-X at topological distance 1
+F01[N-N]	frequency of N-N at topological distance 1
+F01[N-O]	frequency of N-O at topological distance 1
+.........	..........................................................
+F10[Si-X]	frequency of Si-X at topological distance 10
+F10[X-X]	frequency of X-X at topological distance 10
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/XRAY/spacegroups.dat	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4926 @@
+P 1	1
+(X,Y,Z)
+
+P 1-	2
+(X,Y,Z)
+(-X,-Y,-Z)
+
+P -1	2
+(X,Y,Z)
+(-X,-Y,-Z)
+
+P 2	2
+(X,Y,Z)
+(-X,Y,-Z)
+
+P 1 21 1	2
+(X,Y,Z)
+(-X,Y+1/2,-Z)
+
+P 21	2
+(X,Y,Z)
+(-X,Y+1/2,-Z)
+
+C 1 2 1	4
+(X,Y,Z)
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+(-X,Y,-Z)
+(X,1/2-Y,1/2-Z)
+(1/2+Z,1/2+X,Y)
+(Z,1/2-X,1/2-Y)
+(1/2-Z,-X,1/2+Y)
+(-Z,X,-Y)
+(1/2+Y,1/2+Z,X)
+(-Y,Z,-X)
+(Y,1/2-Z,1/2-X)
+(1/2-Y,-Z,1/2+X)
+(1/4+Y,3/4+X,3/4-Z)
+(3/4-Y,3/4-X,1/4-Z)
+(3/4+Y,1/4-X,3/4+Z)
+(1/4-Y,1/4+X,1/4+Z)
+(1/4+X,3/4+Z,3/4-Y)
+(1/4-X,1/4+Z,1/4+Y)
+(3/4-X,3/4-Z,1/4-Y)
+(3/4+X,1/4-Z,3/4+Y)
+(1/4+Z,3/4+Y,3/4-X)
+(3/4+Z,1/4-Y,3/4+X)
+(1/4-Z,1/4+Y,1/4+X)
+(3/4-Z,3/4-Y,1/4-X)
+(1/4-X,1/4-Y,3/4-Z)
+(1/4+X,3/4+Y,1/4-Z)
+(3/4+X,3/4-Y,3/4+Z)
+(3/4-X,1/4+Y,1/4+Z)
+(1/4-Z,1/4-X,3/4-Y)
+(3/4-Z,1/4+X,1/4+Y)
+(1/4+Z,3/4+X,1/4-Y)
+(3/4+Z,3/4-X,3/4+Y)
+(1/4-Y,1/4-Z,3/4-X)
+(3/4+Y,3/4-Z,3/4+X)
+(3/4-Y,1/4+Z,1/4+X)
+(1/4+Y,3/4+Z,1/4-X)
+(1/2-Y,-X,Z)
+(Y,X,1/2+Z)
+(-Y,1/2+X,-Z)
+(1/2+Y,1/2-X,1/2-Z)
+(1/2-X,-Z,Y)
+(1/2+X,1/2-Z,1/2-Y)
+(X,Z,1/2+Y)
+(-X,1/2+Z,-Y)
+(1/2-Z,-Y,X)
+(-Z,1/2+Y,-X)
+(1/2+Z,1/2-Y,1/2-X)
+(Z,Y,1/2+X)
+
+I M -3 M	96
+(X,Y,Z)
+(-X,-Y,Z)
+(-X,Y,-Z)
+(X,-Y,-Z)
+(Z,X,Y)
+(Z,-X,-Y)
+(-Z,-X,Y)
+(-Z,X,-Y)
+(Y,Z,X)
+(-Y,Z,-X)
+(Y,-Z,-X)
+(-Y,-Z,X)
+(Y,X,-Z)
+(-Y,-X,-Z)
+(Y,-X,Z)
+(-Y,X,Z)
+(X,Z,-Y)
+(-X,Z,Y)
+(-X,-Z,-Y)
+(X,-Z,Y)
+(Z,Y,-X)
+(Z,-Y,X)
+(-Z,Y,X)
+(-Z,-Y,-X)
+(-X,-Y,-Z)
+(X,Y,-Z)
+(X,-Y,Z)
+(-X,Y,Z)
+(-Z,-X,-Y)
+(-Z,X,Y)
+(Z,X,-Y)
+(Z,-X,Y)
+(-Y,-Z,-X)
+(Y,-Z,X)
+(-Y,Z,X)
+(Y,Z,-X)
+(-Y,-X,Z)
+(Y,X,Z)
+(-Y,X,-Z)
+(Y,-X,-Z)
+(-X,-Z,Y)
+(X,-Z,-Y)
+(X,Z,Y)
+(-X,Z,-Y)
+(-Z,-Y,X)
+(-Z,Y,-X)
+(Z,-Y,-X)
+(Z,Y,X)
+(1/2+X,1/2+Y,1/2+Z)
+(1/2-X,1/2-Y,1/2+Z)
+(1/2-X,1/2+Y,1/2-Z)
+(1/2+X,1/2-Y,1/2-Z)
+(1/2+Z,1/2+X,1/2+Y)
+(1/2+Z,1/2-X,1/2-Y)
+(1/2-Z,1/2-X,1/2+Y)
+(1/2-Z,1/2+X,1/2-Y)
+(1/2+Y,1/2+Z,1/2+X)
+(1/2-Y,1/2+Z,1/2-X)
+(1/2+Y,1/2-Z,1/2-X)
+(1/2-Y,1/2-Z,1/2+X)
+(1/2+Y,1/2+X,1/2-Z)
+(1/2-Y,1/2-X,1/2-Z)
+(1/2+Y,1/2-X,1/2+Z)
+(1/2-Y,1/2+X,1/2+Z)
+(1/2+X,1/2+Z,1/2-Y)
+(1/2-X,1/2+Z,1/2+Y)
+(1/2-X,1/2-Z,1/2-Y)
+(1/2+X,1/2-Z,1/2+Y)
+(1/2+Z,1/2+Y,1/2-X)
+(1/2+Z,1/2-Y,1/2+X)
+(1/2-Z,1/2+Y,1/2+X)
+(1/2-Z,1/2-Y,1/2-X)
+(1/2-X,1/2-Y,1/2-Z)
+(1/2+X,1/2+Y,1/2-Z)
+(1/2+X,1/2-Y,1/2+Z)
+(1/2-X,1/2+Y,1/2+Z)
+(1/2-Z,1/2-X,1/2-Y)
+(1/2-Z,1/2+X,1/2+Y)
+(1/2+Z,1/2+X,1/2-Y)
+(1/2+Z,1/2-X,1/2+Y)
+(1/2-Y,1/2-Z,1/2-X)
+(1/2+Y,1/2-Z,1/2+X)
+(1/2-Y,1/2+Z,1/2+X)
+(1/2+Y,1/2+Z,1/2-X)
+(1/2-Y,1/2-X,1/2+Z)
+(1/2+Y,1/2+X,1/2+Z)
+(1/2-Y,1/2+X,1/2-Z)
+(1/2+Y,1/2-X,1/2-Z)
+(1/2-X,1/2-Z,1/2+Y)
+(1/2+X,1/2-Z,1/2-Y)
+(1/2+X,1/2+Z,1/2+Y)
+(1/2-X,1/2+Z,1/2-Y)
+(1/2-Z,1/2-Y,1/2+X)
+(1/2-Z,1/2+Y,1/2-X)
+(1/2+Z,1/2-Y,1/2-X)
+(1/2+Z,1/2+Y,1/2+X)
+
+I A -3 D	96
+(X,Y,Z)
+(1/2-X,-Y,1/2+Z)
+(-X,1/2+Y,1/2-Z)
+(1/2+X,1/2-Y,-Z)
+(Z,X,Y)
+(1/2+Z,1/2-X,-Y)
+(1/2-Z,-X,1/2+Y)
+(-Z,1/2+X,1/2-Y)
+(Y,Z,X)
+(-Y,1/2+Z,1/2-X)
+(1/2+Y,1/2-Z,-X)
+(1/2-Y,-Z,1/2+X)
+(3/4+Y,1/4+X,1/4-Z)
+(3/4-Y,3/4-X,3/4-Z)
+(1/4+Y,1/4-X,3/4+Z)
+(1/4-Y,3/4+X,1/4+Z)
+(3/4+X,1/4+Z,1/4-Y)
+(1/4-X,3/4+Z,1/4+Y)
+(3/4-X,3/4-Z,3/4-Y)
+(1/4+X,1/4-Z,3/4+Y)
+(3/4+Z,1/4+Y,1/4-X)
+(1/4+Z,1/4-Y,3/4+X)
+(1/4-Z,3/4+Y,1/4+X)
+(3/4-Z,3/4-Y,3/4-X)
+(-X,-Y,-Z)
+(1/2+X,Y,1/2-Z)
+(X,1/2-Y,1/2+Z)
+(1/2-X,1/2+Y,Z)
+(-Z,-X,-Y)
+(1/2-Z,1/2+X,Y)
+(1/2+Z,X,1/2-Y)
+(Z,1/2-X,1/2+Y)
+(-Y,-Z,-X)
+(Y,1/2-Z,1/2+X)
+(1/2-Y,1/2+Z,X)
+(1/2+Y,Z,1/2-X)
+(1/4-Y,3/4-X,3/4+Z)
+(1/4+Y,1/4+X,1/4+Z)
+(3/4-Y,3/4+X,1/4-Z)
+(3/4+Y,1/4-X,3/4-Z)
+(1/4-X,3/4-Z,3/4+Y)
+(3/4+X,1/4-Z,3/4-Y)
+(1/4+X,1/4+Z,1/4+Y)
+(3/4-X,3/4+Z,1/4-Y)
+(1/4-Z,3/4-Y,3/4+X)
+(3/4-Z,3/4+Y,1/4-X)
+(3/4+Z,1/4-Y,3/4-X)
+(1/4+Z,1/4+Y,1/4+X)
+(1/2+X,1/2+Y,1/2+Z)
+(-X,1/2-Y,Z)
+(1/2-X,Y,-Z)
+(X,-Y,1/2-Z)
+(1/2+Z,1/2+X,1/2+Y)
+(Z,-X,1/2-Y)
+(-Z,1/2-X,Y)
+(1/2-Z,X,-Y)
+(1/2+Y,1/2+Z,1/2+X)
+(1/2-Y,Z,-X)
+(Y,-Z,1/2-X)
+(-Y,1/2-Z,X)
+(1/4+Y,3/4+X,3/4-Z)
+(1/4-Y,1/4-X,1/4-Z)
+(3/4+Y,3/4-X,1/4+Z)
+(3/4-Y,1/4+X,3/4+Z)
+(1/4+X,3/4+Z,3/4-Y)
+(3/4-X,1/4+Z,3/4+Y)
+(1/4-X,1/4-Z,1/4-Y)
+(3/4+X,3/4-Z,1/4+Y)
+(1/4+Z,3/4+Y,3/4-X)
+(3/4+Z,3/4-Y,1/4+X)
+(3/4-Z,1/4+Y,3/4+X)
+(1/4-Z,1/4-Y,1/4-X)
+(1/2-X,1/2-Y,1/2-Z)
+(X,1/2+Y,-Z)
+(1/2+X,-Y,Z)
+(-X,Y,1/2+Z)
+(1/2-Z,1/2-X,1/2-Y)
+(-Z,X,1/2+Y)
+(Z,1/2+X,-Y)
+(1/2+Z,-X,Y)
+(1/2-Y,1/2-Z,1/2-X)
+(1/2+Y,-Z,X)
+(-Y,Z,1/2+X)
+(Y,1/2+Z,-X)
+(3/4-Y,1/4-X,1/4+Z)
+(3/4+Y,3/4+X,3/4+Z)
+(1/4-Y,1/4+X,3/4-Z)
+(1/4+Y,3/4-X,1/4-Z)
+(3/4-X,1/4-Z,1/4+Y)
+(1/4+X,3/4-Z,1/4-Y)
+(3/4+X,3/4+Z,3/4+Y)
+(1/4-X,1/4+Z,3/4-Y)
+(3/4-Z,1/4-Y,1/4+X)
+(1/4-Z,1/4+Y,3/4-X)
+(1/4+Z,3/4-Y,1/4-X)
+(3/4+Z,3/4+Y,3/4+X)
+
+B 2	4
+(X,Y,Z)
+(-X,-Y,Z)
+(1/2+X,+Y,1/2+Z)
+(1/2-X,-Y,1/2+Z)
+
+P 1 1 21	2
+(X,Y,Z)
+(-X,-Y,1/2+Z)
+
+P 2 21 21	4
+(X,Y,Z)
+(X,-Y,-Z)
+(-X,1/2+Y,1/2-Z)
+(-X,1/2-Y,1/2+Z)
+
+P 21 2 21	4
+(X,Y,Z)
+(-X,Y,-Z)
+(1/2+X,-Y,1/2-Z)
+(1/2-X,-Y,1/2+Z)
+
+I 1 2 1	4
+(X,Y,Z)
+(-X,Y,-Z)
+(1/2+X,1/2+Y,1/2+Z)
+(1/2-X,1/2+Y,1/2-Z)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/atomtyping/AMBERTypes.dat	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,61 @@
+CT	6	4	*	*	*						*
+C	6	3	*	*	*						(XA1)
+CN	6	3	*	*	[RG5,RG6,AR1.AR2.AR3]	(C3,C3,N3(H))
+CB	6	3	*	*	[RG5,RG6,AR1.AR2.AR3]	*
+CR	6	3	*	*	[RG5,AR1.AR2.AR3]		(N3,N3)
+CR	6	3	*	*	[RG5,AR1.AR2.AR3]		(N2,N3(H))
+CK	6	3	*	*	[RG5,AR1.AR2.AR3]		(N2,N3)
+CC	6	3	0	*	[RG5,AR1.AR2.AR3]		(C3,N3(C3,H))
+CC	6	3	0	*	[RG5,AR1.AR2.AR3]		(C3,N2(C3))
+CW	6	3	*	*	[RG5,AR1.AR2.AR3]		(C3,N3(H))
+CV	6	3	*	*	[RG5,AR1.AR2.AR3]		(C3,N2)
+C*	6	3	*	*	[RG5,AR1.AR2.AR3]		(C3,C3)
+CQ	6	3	*	*	[RG6,AR1.AR2.AR3]		(N2,N2)
+CM	6	3	*	*	[RG6,AR1.AR2.AR3]		(C3,C3(N2(C3(N3(C3)))))
+CM	6	3	*	*	[RG6,AR1.AR2.AR3]		(C3,C3(N3(C3(N3(C3)))))
+CM	6	3	*	*	[RG6,AR1.AR2.AR3]		(C3,N3(C3(N2(C3(C3)))))
+CM	6	3	*	*	[RG6,AR1.AR2.AR3]		(N3,C3(C3(N3(C3(N3)))))
+CA	6	3	*	*	[AR1.AR2.AR3]			*
+CD	6	3	*	*	*						(C3,C3)
+CM	6	3	*	*	*						*
+CZ	6	2	*	*	*						*
+H	1	1	*	*	*						(N)
+HS	1	1	*	*	*						(S)
+HP	1	1	*	*	*						(C(N4))
+HW	1	1	*	*	*						(O(H1))
+HO	1	1	*	*	*						(O)
+H1	1	1	*	1	*						(C4)
+H2	1	1	*	2	*						(C4)
+H3	1	1	*	3	*						(C4)
+HC	1	1	*	*	*						(C4)
+H4	1	1	*	1	*						(XX[AR1.AR2.AR3])
+H5	1	1	*	2	*						(XX[AR1.AR2.AR3])
+HA	1	1	*	*	*						(XX[AR1.AR2.AR3])
+F	9	1	*	*	*						*
+Cl	17	1	*	*	*						*
+Br	35	1	*	*	*						*
+I	53	1	*	*	*						*
+N1	7	1	*	*	*						*
+NB	7	2	*	*	[RG5,AR1.AR2.AR3]		*
+NC	7	2	*	*	[RG6,AR1.AR2.AR3]		*
+N2	7	-1	*	*	*						(C3(N3,N3))
+NO	7	-1	*	*	*						(O1,O1)
+NA	7	3	1	*	[RG5.RG6,AR1.AR2.AR3]	*
+N2	7	3	*	*	[NR]					(XX[AR1.AR2.AR3])
+N*	7	3	*	*	[AR1.AR2.AR3]			*
+N	7	3	*	*	*						(C3(XA1))
+NT	7	3	*	*	*						*
+N3	7	4	*	*	*						*
+O2	8	1	*	*	*						(C(O1))
+O2	8	1	*	*	*						(P)
+O	8	1	*	*	*						(C)
+O	8	1	*	*	*						(S)
+OH	8	2	1	*	*						*
+OW	8	2	2	*	*						*
+OS	8	2	*	*	*						*
+SH	16	2	1	*	*						*
+SH	16	2	2	*	*						*
+S	16	2	*	*	*						*
+SO	16	4	*	*	*						*
+LP	0	-1	*	*	*						*
+DU	-1	-1	*	*	*						*
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/atomtyping/GAFFTypes.dat	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,208 @@
+cx    6   4   *   *   [RG3]       *
+cy    6		4   *   *   [RG4]       *
+c3    6   4   *		*		*						*
+c     6   3   *   *   [2DL]   		(XA1)
+c     6   3   *   *   [1DB,0DL]  	(XA1)
+c     6   3   *   *   [3sb]   		(XA1)
+cz    6   3   *   *   *           (N3,N3,N3)
+cp    6   3   *   *   [AR1,1RG6]  (XX[AR1],XX[AR1],XX[AR1])
+ca    6   3   *   *   [AR1]    		*
+cc    6   3   *   *   [sb,db,AR2]       (C3(C3))
+cc    6   3   *   *   [sb,db,AR2]       (C3(C2))
+cc    6   3   *   *   [sb,db,AR2]       (C3(XB2))
+cc    6   3   *   *   [sb,db,AR2]       (XB2(XB2))
+cc    6   3   *   *   [sb,db,AR2]       (XB2(C2))
+cc    6   3   *   *   [sb,db,AR2]       (XB2(C3))
+cc    6   3   *   *   [sb,db,AR2]       (C3[sb'])
+cc    6   3   *   *   [sb,db,AR2]       (XB2[sb'])
+cc    6   3   *   *   [sb,db,AR2]       (XD3[sb',db])
+cc    6   3   *   *   [sb,db,AR2]       (XD4[sb',db])
+cc    6   3   *   *   [sb,db,AR3]       (C3(C3))
+cc    6   3   *   *   [sb,db,AR3]       (C3(C2))
+cc    6   3   *   *   [sb,db,AR3]       (C3(XB2))
+cc   	6   3   *   *   [sb,db,AR3]       (XB2(XB2))
+cc    6   3   *   *   [sb,db,AR3]       (XB2(C2))
+cc    6   3   *   *   [sb,db,AR3]       (XB2(C3))
+cc    6   3   *   *   [sb,db,AR3]       (C3[sb'])
+cc    6   3   *   *   [sb,db,AR3]       (XB2[sb'])
+cc    6   3   *   *   [sb,db,AR3]       (XD3[sb',db])
+cc    6   3   *   *   [sb,db,AR3]       (XD4[sb',db])
+ce    6   3   *   *   [sb,db]          (C3[SB'])
+ce    6   3   *   *   [sb,db]          (C2[SB'])
+ce    6   3   *   *   [sb,db]          (XB2[SB'])
+ce    6   3   *   *   [sb,db]          (XD3[SB',db])
+ce    6   3   *   *   [sb,db]          (XD4[SB',db])
+cu    6   3   *   *   [RG3]       *
+cv    6   3   *   *   [RG4]       *
+c2    6   3   *		*		*						*
+cg    6   2   *   *   [sb,tb]          (C2[SB'])
+cg    6   2   *   *   [sb,tb]          (C3[SB'])
+cg    6   2   *   *   [sb,tb]          (N1[SB'])
+cg    6   2   *   *   [sb,tb]          (XB2[SB'])
+c1    6   2   *		*		*						*
+c1    6   1   *		*		*						*
+hn    1   1   *   *   *       		(N)
+ho    1   1   *   *   *       		(O)
+hs    1   1   *   *   *       		(S)
+hp    1   1   *   *   *       		(P)
+hx    1   1   *   *   *       		(C(N4))
+hw    1   1   *   *   *       		(O(H1))
+h3    1   1   *		3   *       		(C4)
+h2    1   1   *   2   *       		(C4)
+h1    1   1   *   1   *       		(C4)
+hc    1   1   *   *   *       		(C4)
+h5    1   1   *   2   *       		(C3)
+h4    1   1   *   1   *       		(C3)
+ha    1   1   *		*		*						*
+f     9  -1		*		*		*						*
+cl    17 -1		*		*		*						*
+br    35 -1		*		*		*						*
+i     53 -1		*		*		*						*
+pc    15  2   *   *   [sb,db,AR2]       (C3(C3))
+pc    15  2   *   *   [sb,db,AR2]       (C3(C2))
+pc    15  2   *   *   [sb,db,AR2]       (C3(XB2))
+pc    15  2   *   *   [sb,db,AR2]       (XB2(C3))
+pc    15  2   *   *   [sb,db,AR2]       (XB2(C2))
+pc    15  2   *   *   [sb,db,AR2]       (XB2(XB2))
+pc    15  2   *   *   [sb,db,AR2]       (C3[sb'])
+pc    15  2   *   *   [sb,db,AR2]       (C2[sb'])
+pc    15  2   *   *   [sb,db,AR2]       (XB2[sb'])
+pc    15  2   *   *   [sb,db,AR2]       (XD3[sb',db])
+pc    15  2   *   *   [sb,db,AR2]       (XD4[sb',db])
+pc    15  2   *   *   [sb,db,AR3]       (C3(C3))
+pc    15  2   *   *   [sb,db,AR3]       (C3(C2))
+pc    15  2   *   *   [sb,db,AR3]       (C3(XB2))
+pc    15  2   *   *   [sb,db,AR3]       (XB2(C3))
+pc    15  2   *   *   [sb,db,AR3]       (XB2(C2))
+pc    15  2   *   *   [sb,db,AR3]       (XB2(XB2))
+pc   	15  2   *   *   [sb,db,AR3]       (C3[sb'])
+pc    15  2   *   *   [sb,db,AR3]       (C2[sb'])
+pc    15  2   *   *   [sb,db,AR3]       (XB2[sb'])
+pc    15  2   *   *   [sb,db,AR3]       (XD3[sb',db])
+pc    15  2   *   *   [sb,db,AR3]       (XD4[sb',db])
+pb    15  2   *   *   [AR1]        *
+pe    15  2   *   *   [sb,db]          (C3[sb'])
+pe    15  2   *   *   [sb,db]          (C2[SB'])
+pe    15  2   *   *   [sb,db]          (XA1[SB'])
+pe    15  2   *   *   [sb,db]          (XB2[SB'])
+pe    15  2   *   *   [sb,db]          (XD3[SB',DB])
+pe    15  2   *   *   [sb,db]          (XD4[SB',DB])
+p2    15  2   *		*		*						*
+p2    15  1   *		*		*						*
+px    15  3   *   *   [db]    		(XB2[sb'])
+px    15  3   *   *   [db]    		(C3[sb'])
+px    15  3   *   *   [db]    		(XD3[sb',db])
+px    15  3   *   *   [db]    		(XD4[sb',db])
+p4    15  3   *   *   [db]    		(XA1)
+p3    15  3   *		*		*						*
+py    15  4   *   *   [db]    		(XB2[sb'])
+py    15  4   *   *   [db]    		(C3[sb'])
+py    15  4   *   *   [db]    		(XD3[sb',db])
+py    15  4   *   *   [db]    		(XD4[sb',db])
+p5    15  4   *		*		*						*
+p5    15  5   *		*		*						*
+p5    15  6   *		*		*						*
+n     7   3   *   *   *       		(C3(XA1))
+n4    7   4   *		*		*						*
+no    7   3   *   *   *       		(O1,O1)
+na    7   3   *   *   [AR1.AR2.AR3]    *
+nh    7   3   *   *   *       		(XX[AR1.AR2.AR3])
+nh    7   3   *   *   *       		(C3[DB])
+nh    7   3   *   *   *       		(N2[DB])
+nh    7   3   *   *   *       		(P2[DB])
+n3    7   3   *		*		*						*
+nb    7   2   *   *   [AR1]       *
+nc    7   2   *   *   [sb,db,AR2]       (C3(C3))
+nc    7   2   *   *   [sb,db,AR2]       (C3(C2))
+nc    7   2   *   *   [sb,db,AR2]       (C3(XB2))
+nc    7   2   *   *   [sb,db,AR2]       (XB2(C3))
+nc    7   2   *   *   [sb,db,AR2]       (XB2(C2))
+nc    7   2   *   *   [sb,db,AR2]       (XB2(XB2))
+nc    7   2   *   *   [sb,db,AR2]       (C3[sb'])
+nc    7   2   *   *   [sb,db,AR2]       (XB2[sb'])
+nc    7   2   *   *   [sb,db,AR2]       (XD3[sb',db])
+nc    7   2   *   *   [sb,db,AR2]       (XD4[sb',db])
+nc    7   2   *   *   [sb,db,AR3]       (C3(C3))
+nc    7   2   *   *   [sb,db,AR3]       (C3(C2))
+nc    7   2   *   *   [sb,db,AR3]       (C3(XB2))
+nc    7   2   *   *   [sb,db,AR3]       (XB2(C3))
+nc    7   2   *   *   [sb,db,AR3]       (XB2(C2))
+nc    7   2   *   *   [sb,db,AR3]       (XB2(XB2))
+nc    7   2   *   *   [sb,db,AR3]       (C3[sb'])
+nc    7   2   *   *   [sb,db,AR3]       (XB2[sb'])
+nc    7   2   *   *   [sb,db,AR3]       (XD3[sb',db])
+nc    7   2   *   *   [sb,db,AR3]       (XD4[sb',db])
+ne    7   2   *   *   [sb,db]          (C2[SB'])
+ne    7   2   *   *   [sb,db]          (C3[SB'])
+ne    7   2   *   *   [sb,db]          (XA1[SB'])
+ne    7   2   *   *   [sb,db]          (XB2[SB'])
+ne    7   2   *   *   [sb,db]          (XD3[SB',db])
+ne    7   2   *   *   [sb,db]          (XD4[SB',db])
+n1    7   2   *   *   [2db]             *
+n1    7   2   *   *   [tb,sb]           *
+n2    7   2   *		*		*									*
+n1    7   1   *		*		*									*
+o     8   1   *		*		*									*
+oh    8   2   1   *		*									*
+oh    8   2   2   *		*									*
+oh    8   3   1   *		*									*
+oh    8   3   2   *		*									*
+oh    8   3   3   *		*									*
+os    8   2   *		*		*									*
+os    8   3   *		*		*									*
+os    8  -1		*		*		*									*
+s     16  1   *		*		*									*
+s2    16  2   *   *   [DB]              *
+s2    16  2   *   *   [TB]              *
+sh    16  2   1   *		*									*
+sh    16  2   2   *		*									*
+ss   	16  2   *		*		*									*
+sx    16  3   *   *   [db]    		(XB2[sb'])
+sx    16  3   *   *   [db]    		(C3[sb'])
+sx    16  3   *   *   [db]    		(XD3[sb',db])
+sx    16  3   *   *   [db]    		(XD4[sb',db])
+s4    16  3   *		*		*						*
+sy    16  4   *   *   [db]    		(XB2[sb'])
+sy    16  4   *   *   [db]    		(C3[sb'])
+sy    16  4   *   *   [db]    		(XD3[sb',db])
+sy    16  4   *   *   [db]    		(XD4[sb',db])
+s6    16  4   *		*		*						*
+s6    16  5   *		*		*						*
+s6    16  6   *		*		*						*
+Li    3  -1		*		*		*						*
+Be    4  -1		*		*		*						*
+B     5  -1		*		*		*						*
+Na    11 -1		*		*		*						*
+Mg    12 -1		*		*		*						*
+Al    13 -1 	*		*		*						*
+Si    14 -1 	*		*		*						*
+K     19 -1		*		*		*						*
+Ca    20 -1		*		*		*						*
+Sr    38 -1		*		*		*						*
+Ba   	56 -1		*		*		*						*
+Sc    21 -1		*		*		*						*
+Ti    22 -1		*		* 	*						*
+V     23 -1		*		*		*						*
+Cr    24 -1		*		*		*						*
+Mn    25 -1		*		*		*						*
+Fe    26 -1		*		*		*						*
+Co    27 -1		*		*		*						*
+Ni    28 -1		*		*		*						*
+Cu    29 -1		*		*		*						*
+Zn    30 -1		*		*		*						*
+Ga    31 -1		*		*		*						*
+Ge    32 -1		*		*		*						*
+As    33 -1		*		*		*						*
+Se    34 -1		*		*		*						*
+Ru    44 -1		*		*		*						*
+Rh    45 -1		*		*		*						*
+Pd    46 -1		*		*		*						*
+Ag    47 -1		*		*		*						*
+Cd    48 -1		*		*		*						*
+Pt    78 -1		*		*		*						*
+Au    79 -1		*		*		*						*
+Hg    80 -1	  *		*		*						*
+Tl    81 -1	  *		*		*						*
+Pb    82 -1	  *		*		*						*
+lp    0   1   *   *		*						*
+DU    -1 -1		*   *		*						*
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/atomtyping/SYBYLTypes.dat	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,66 @@
+C.3	6	4	*	*	*	*
+C.cat	6	3	*	*	*	(N3,N3,N3)
+C.ar	6	3	*	*	[AR1]	*
+C.2	6	3	*	*	*	*
+C.1	6	2	*	*	*	*
+C.1	6	1	*	*	*	*
+H	1	-1	*	*	*	*
+F	9	-1	*	*	*	*
+Cl	17	-1	*	*	*	*
+Br	35	-1	*	*	*	*
+I	53	-1	*	*	*	*
+P.3	15	-1	*	*	*	*
+N.4	7	4	*	*	*	*
+N.am	7	3	*	*	*	(C3(XA1))
+N.pl3	7	3	*	*	*	(O1,O1)
+N.pl3	7	3	*	*	[AR1.AR2.AR3]	*
+N.3	7	3	*	*	*	*
+N.ar	7	2	*	*	[AR1]	*
+N.2	7	2	*	*	*	*
+N.1	7	1	*	*	*	*
+O.co2	8	1	*	*	*	(C3(O1))
+O.co2	8	1	*	*	*	(P(O1))
+O.2	8	1	*	*	*	*
+O.3	8	2	*	*	*	*
+S.2	16	1	*	*	*	*
+S.3	16	2	*	*	*	*
+S.o	16	3	*	*	*	(O1[DB'])
+S.o2	16	4	*	*	*	(O1[DB'],O1[DB'])
+s.3	16	-1	*	*	*	*
+Li	3	-1	*	*	*	*
+Be	4	-1	*	*	*	*
+B	5	-1	*	*	*	*
+Na	11	-1	*	*	*	*
+Mg	12	-1	*	*	*	*
+Al	13	-1	*	*	*	*
+Si	14	-1	*	*	*	*
+K	19	-1	*	*	*	*
+Ca	20	-1	*	*	*	*
+Sr	38	-1	*	*	*	*
+Ba	56	-1	*	*	*	*
+Sc	21	-1	*	*	*	*
+Ti	22	-1	*	*	*	*
+V	23	-1	*	*	*	*
+Cr	24	-1	*	*	*	*
+Mn	25	-1	*	*	*	*
+Fe	26	-1	*	*	*	*
+Co	27	-1	*	*	*	*
+Ni	28	-1	*	*	*	*
+Cu	29	-1	*	*	*	*
+Zn	30	-1	*	*	*	*
+Ga	31	-1	*	*	*	*
+Ge	32	-1	*	*	*	*
+As	33	-1	*	*	*	*
+Se	34	-1	*	*	*	*
+Ru	44	-1	*	*	*	*
+Rh	45	-1	*	*	*	*
+Pd	46	-1	*	*	*	*
+Ag	47	-1	*	*	*	*
+Cd	48	-1	*	*	*	*
+Pt	78	-1	*	*	*	*
+Au	79	-1	*	*	*	*
+Hg	80	-1	*	*	*	*
+Tl	81	-1	*	*	*	*
+Pb	82	-1	*	*	*	*
+lp	0	1	*	*	*	*
+ANY	-1	-1	*	*	*	*	*
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/BondOrder.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,366 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<table>
+	<!-- 	This file supplies improved penalty scores for different
+	  		atom types in bond type perception based on the work of
+
+	 				Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and
+	 				bond type perception in molecular mechanical calculations". Journal of
+	 				Molecular Graphics and Modelling , 25, 2006, 247260
+
+				A penalty score of 0 means that the corresponding valence is optimal.
+				Note that the first matching entry is taken as the final atom type.
+
+				Note that in the SMARTS strings we use atomic numbers rather than symbols (e.g. #8 instead of O).
+				The reason is that wrongly assigned aromatic bonds in the input would lead to failure to identify the
+				right rule!
+	-->
+	<!-- for charged H -->
+	<entry id="0">
+		<elementstring>H</elementstring>
+		<smartstring>SMARTS([#1+])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="1">
+		<elementstring>H</elementstring>
+		<smartstring>SMARTS([#1])</smartstring>
+		<penalty valence="1">0</penalty>
+	</entry>
+	<entry id="2">
+		<elementstring>F</elementstring>
+		<smartstring>SMARTS(F)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="4">
+		<elementstring>Br</elementstring>
+		<smartstring>SMARTS(Br)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="5">
+		<elementstring>I</elementstring>
+		<smartstring>SMARTS(I)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="6"> <!-- 	SMARTS([CD1]~[ND2]) AND element(C)</smartstring> -->
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([$([#6D1](~[#7D2]))])</smartstring>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">32</penalty>
+	</entry>
+	<entry id="7">
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([#6D1])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">32</penalty>
+	</entry>
+	<entry id="9">
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([#6])</smartstring>
+		<penalty valence="2">64</penalty>
+		<penalty valence="3">32</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">32</penalty>
+		<penalty valence="6">64</penalty>
+	</entry>
+	<entry id="10">
+		<elementstring>Si</elementstring>
+		<smartstring>SMARTS(Si)</smartstring>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="11">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D1](~[#7D2]))])</smartstring> <!--SMARTS([ND1]~[ND2]) AND SMARTS([ND1])</smartstring> -->
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">0</penalty>
+	</entry>
+	<entry id="12">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D1])</smartstring>
+		<penalty valence="2">3</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">32</penalty>
+	</entry>
+	<entry id="13">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D2](~[#7D1]))])</smartstring> <!--SMARTS([ND1]~[ND2]) AND SMARTS([ND2])</smartstring> -->
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="14">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D2])</smartstring>
+		<penalty valence="2">4</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">2</penalty>
+	</entry>
+	<entry id="151"><!-- for charged N in  O == N+ __ O- -->
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D3](~[#8D1-,#16D1-])~[#8D1,#16D1])])</smartstring>
+		<penalty valence="3">32</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">32</penalty>
+		<penalty valence="6">64</penalty>
+	</entry>
+	<entry id="15">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])~[#8D1,#16D1])])</smartstring>
+		<penalty valence="3">64</penalty>
+		<penalty valence="4">32</penalty>
+		<penalty valence="5">0</penalty>
+		<penalty valence="6">32</penalty>
+	</entry>
+	<entry id="16">
+		<elementstring>N</elementstring>
+		<!-- <smartstring>SMARTS([$(*OD1)&amp;$(*aR)&amp;n]) OR SMARTS([$(*OD1);$(*R);N])</smartstring> -->
+		<smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="17">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D3])</smartstring>
+		<penalty valence="2">32</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">2</penalty>
+	</entry>
+	<entry id="181"><!-- for charged N in   N+ H_4 -->
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D4+])</smartstring>
+		<penalty valence="3">32</penalty>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="18">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D4])</smartstring>
+		<penalty valence="2">64</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">64</penalty>
+	</entry>
+	<entry id="182">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D5])</smartstring>
+		<penalty valence="5">0</penalty>
+	</entry>
+	<entry id="191"><!-- for charged O- -->
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#8D1-])</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">32</penalty>
+	</entry>
+	<entry id="192">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([$([#8D1](~[#6D3]~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">0</penalty>
+	</entry>
+	<entry id="19">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])) AND element(O)</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">1</penalty>
+	</entry>
+	<entry id="20">
+		<elementstring>O</elementstring>
+		<smartstring> SMARTS([#8D1])</smartstring>
+		<penalty valence="1">1</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="21">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#8D2])</smartstring>
+		<penalty valence="1">32</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="211">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#8D3])</smartstring>
+		<penalty valence="3">0</penalty>
+	</entry>
+	<entry id="22">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS(#15D1)</smartstring>
+		<penalty valence="2">2</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">32</penalty>
+	</entry>
+	<entry id="23">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS(#15D2)</smartstring>
+		<penalty valence="2">4</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">2</penalty>
+	</entry>
+	<entry id="24">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS(#15D3)</smartstring>
+		<penalty valence="2">32</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">2</penalty>
+	</entry>
+	<entry id="251">
+		<elementstring>P</elementstring>
+		<!-- Note: this is _SLOW_ -->
+		<smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1,#8D1-,#16D1-])(~[#8D1-,#16D1-]))])</smartstring>
+		<penalty valence="5">0</penalty>
+		<penalty valence="6">32</penalty>
+	</entry>
+	<entry id="25">
+		<elementstring>P</elementstring>
+		<!-- Note: this is _SLOW_ -->
+		<smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])(~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="5">32</penalty>
+		<penalty valence="6">0</penalty>
+		<penalty valence="7">32</penalty>
+	</entry>
+	<entry id="26">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="6">32</penalty>
+		<penalty valence="7">0</penalty>
+	</entry>
+	<entry id="27">
+		<elementstring>P</elementstring>
+		<!-- This rule should be the last PD4 rule because it should only match when the other rules fail! -->
+		<smartstring>SMARTS(#15D4)</smartstring>
+		<penalty valence="3">64</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">0</penalty>
+		<penalty valence="6">32</penalty>
+	</entry>
+	<entry id="28">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#7D3](~[#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])) AND element(S)</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">1</penalty>
+		</entry>
+	<entry id="291">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([$([#16D1](~[#6D3]~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">0</penalty>
+	</entry>
+	<entry id="29">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D1])</smartstring>
+		<penalty valence="1">2</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="30">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D2])</smartstring>
+		<penalty valence="1">2</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="31">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D3])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">2</penalty>
+		<penalty valence="6">2</penalty>
+	</entry>
+	<entry id="32">
+		<elementstring>S</elementstring>
+		<smartstring>	SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="6">0</penalty>
+		<penalty valence="7">32</penalty>
+		</entry>
+	<entry id="331"><!--for a charged O in SO_4 -->
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([$([#16D4](~[#8D1-,#16D1-])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="6">0</penalty>
+	</entry>
+	<entry id="33">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="6">32</penalty>
+		<penalty valence="7">0</penalty>
+	</entry>
+	<entry id="34">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="6">32</penalty>
+		<penalty valence="7">0</penalty>
+	</entry>
+	<entry id="35">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D4])</smartstring>
+		<penalty valence="4">4</penalty>
+		<penalty valence="5">2</penalty>
+		<penalty valence="6">0</penalty>
+		</entry>
+	<entry id="36">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D5])</smartstring>
+		<penalty valence="5">2</penalty>
+		<penalty valence="6">0</penalty>
+	</entry>
+<!-- The following rules are added to cope with ions -->
+	<entry id="40">
+		<elementstring>Li</elementstring>
+		<smartstring>SMARTS([#3])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="41">
+		<elementstring>Na</elementstring>
+		<smartstring>SMARTS([#11])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="42">
+		<elementstring>Mg</elementstring>
+		<smartstring>SMARTS([#12])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="43">
+		<elementstring>K</elementstring>
+		<smartstring>SMARTS([#19])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="44">
+		<elementstring>Ca</elementstring>
+		<smartstring>SMARTS([#20])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="45">
+		<elementstring>Cu</elementstring>
+		<smartstring>SMARTS([#29])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="46">
+		<elementstring>Zn</elementstring>
+		<smartstring>SMARTS([#30])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="47">
+		<elementstring>Fe</elementstring>
+		<smartstring>SMARTS([#26])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="48">
+		<elementstring>Cl</elementstring>
+		<smartstring>SMARTS([#17-])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="49">
+		<elementstring>Cl</elementstring>
+		<smartstring>SMARTS([#17])</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+		<penalty valence="3">128</penalty>
+		<penalty valence="4">128</penalty>
+	</entry>
+</table>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/BondOrderGAFF.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,306 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<table>
+	<!-- 	This file supplies penalty scores for different
+	  		atom types in bond type perception accoring to
+
+	 				Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and
+	 				bond type perception in molecular mechanical calculations". Journal of
+	 				Molecular Graphics and Modelling , 25, 2006, 247260
+
+				A penalty score of 0 means that the corresponding valence is optimal.
+				Note that the first matching entry is taken as the final atom type.
+
+				Note that in the SMARTS strings we use atomic numbers rather than symbols (e.g. #8 instead of O).
+				The reason is that wrongly assigned aromatic bonds in the input would lead to failure to identify the
+				right rule!
+
+	 			Rev 14.12.2007  Conversion was done by Anna Dehof
+ -->
+	<entry id="1">
+		<elementstring>H</elementstring>
+		<smartstring>SMARTS([#1])</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="2">
+		<elementstring>F</elementstring>
+		<smartstring>SMARTS(F)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="3">
+		<elementstring>Cl</elementstring>
+		<smartstring>SMARTS(Cl)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="4">
+		<elementstring>Br</elementstring>
+		<smartstring>SMARTS(Br)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="5">
+		<elementstring>I</elementstring>
+		<smartstring>SMARTS(I)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="6">
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([$([#6D1](~[#7D2]))])</smartstring>
+		<!--SMARTS([CD1]~[ND2]) AND element(C)</smartstring> -->
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">32</penalty>
+	</entry>
+	<entry id="7">
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([#6D1])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">32</penalty>
+	</entry>
+	<entry id="8">
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([$([#6D3](~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="4">32</penalty>
+		<penalty valence="5">0</penalty>
+		<penalty valence="6">32</penalty>
+	</entry>
+	<entry id="9">
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([#6])</smartstring>
+		<penalty valence="2">64</penalty>
+		<penalty valence="3">32</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">32</penalty>
+		<penalty valence="6">64</penalty>
+	</entry>
+	<entry id="10">
+		<elementstring>Si</elementstring>
+		<smartstring>SMARTS([#14])</smartstring>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="11">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D1](~[#7D2]))])</smartstring>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">0</penalty>
+	</entry>
+	<entry id="12">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D1])</smartstring>
+		<penalty valence="2">3</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">32</penalty>
+	</entry>
+	<entry id="13">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D2](~[#7D1]))])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="14">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D2])</smartstring>
+		<penalty valence="2">4</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">2</penalty>
+	</entry>
+	<entry id="15">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])~[#8D1,#16D1])])</smartstring>
+		<penalty valence="3">64</penalty>
+		<penalty valence="4">32</penalty>
+		<penalty valence="5">0</penalty>
+		<penalty valence="6">32</penalty>
+	</entry>
+	<entry id="16">
+		<elementstring>N</elementstring>
+		<!-- <smartstring>SMARTS([$(*OD1)&amp;$(*aR)&amp;n]) OR SMARTS([$(*OD1);$(*R);N])</smartstring> -->
+		<smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="17">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D3])</smartstring>
+		<penalty valence="2">32</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">2</penalty>
+	</entry>
+	<entry id="18">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D4])</smartstring>
+		<penalty valence="2">64</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">64</penalty>
+	</entry>
+	<entry id="19">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])) AND element(O)</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">1</penalty>
+	</entry>
+	<entry id="20">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#8D1])</smartstring>
+		<penalty valence="1">1</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="21">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#8D2])</smartstring>
+		<penalty valence="1">32</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="22">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS(#15D1)</smartstring>
+		<penalty valence="2">2</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">32</penalty>
+	</entry>
+	<entry id="23">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS(#15D2)</smartstring>
+		<penalty valence="2">4</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">2</penalty>
+	</entry>
+	<entry id="24">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS(#15D3)</smartstring>
+		<penalty valence="2">32</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">2</penalty>
+	</entry>
+	<entry id="25">
+		<elementstring>P</elementstring>
+		<!-- Note: this is _SLOW_ -->
+		<smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])(~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="5">32</penalty>
+		<penalty valence="6">0</penalty>
+		<penalty valence="7">32</penalty>
+	</entry>
+	<entry id="26">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="6">32</penalty>
+		<penalty valence="7">0</penalty>
+	</entry>
+	<entry id="27">
+		<elementstring>P</elementstring>
+		<!-- This rule should be the last PD4 rule because it should only match when the other rules fail! -->
+		<smartstring>SMARTS(#15D4)</smartstring>
+		<penalty valence="3">64</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">0</penalty>
+		<penalty valence="6">32</penalty>
+	</entry>
+	<entry id="28">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#7D3](~[#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])) AND element(S)</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">1</penalty>
+	</entry>
+	<entry id="29">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D1])</smartstring>
+		<penalty valence="1">2</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="30">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D2])</smartstring>
+		<!-- These are the penalties given in the GAFF - paper; unfortunately, the values implemented in antechamber are different!
+		<penalty valence="1">32</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">32</penalty>
+		<penalty valence="4">1</penalty> -->
+		<penalty valence="1">2</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="31">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D3])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">2</penalty>
+		<penalty valence="6">2</penalty>
+	</entry>
+	<entry id="32">
+		<elementstring>S</elementstring>
+		<smartstring>	SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="6">0</penalty>
+		<penalty valence="7">32</penalty>
+	</entry>
+	<entry id="33">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="6">32</penalty>
+		<penalty valence="7">0</penalty>
+	</entry>
+	<entry id="34">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="6">32</penalty>
+		<penalty valence="7">0</penalty>
+	</entry>
+	<entry id="35">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D4])</smartstring>
+		<penalty valence="4">4</penalty>
+		<penalty valence="5">2</penalty>
+		<penalty valence="6">0</penalty>
+	</entry>
+	<!-- The following rules are added to cope with ions -->
+	<entry id="40">
+		<elementstring>Li</elementstring>
+		<smartstring>SMARTS([#3])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="41">
+		<elementstring>Na</elementstring>
+		<smartstring>SMARTS([#11])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="42">
+		<elementstring>Mg</elementstring>
+		<smartstring>SMARTS([#12])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="43">
+		<elementstring>K</elementstring>
+		<smartstring>SMARTS([#19])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="44">
+		<elementstring>Ca</elementstring>
+		<smartstring>SMARTS([#20])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="45">
+		<elementstring>Cu</elementstring>
+		<smartstring>SMARTS([#29])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="46">
+		<elementstring>Zn</elementstring>
+		<smartstring>SMARTS([#30])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+
+</table>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/bond_lengths.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,257 @@
+<node>BondLengthsDB
+	<node>1
+		<node>Names
+			<node>Hydrogen</node>
+			<node>H</node>
+		</node>
+		<node>Partners
+			<node>6
+				<node>BondLengths
+					<node>max<value>1.15</value></node>
+					<node>single<value>1.09</value></node>
+					<node>min<value>0.95</value></node>
+				</node>
+			</node>
+			<node>7
+				<node>BondLengths
+					<node>max<value>1.10</value></node>
+					<node>single<value>1.03</value></node>
+					<node>min<value>0.9</value></node>
+				</node>
+			</node>
+			<node>8
+				<node>BondLengths
+					<node>max<value>1.1</value></node>
+					<node>single<value>0.96</value></node>
+					<node>min<value>0.9</value></node>
+				</node>
+			</node>
+			<node>15
+				<node>BondLengths
+					<node>max<value>1.5</value></node>
+					<node>single<value>1.0</value></node>
+					<node>min<value>0.9</value></node>
+				</node>
+			</node>
+			<node>16
+				<node>BondLengths
+					<node>max<value>1.5</value></node>
+					<node>single<value>1.34</value></node>
+					<node>min<value>1.1</value></node>
+				</node>
+			</node>
+		</node>
+	</node>
+	<node>6
+		<node>Names
+			<node>Carbon</node>
+			<node>C</node>
+		</node>
+		<node>Partners
+			<node>6
+				<node>BondLengths
+					<node>max<value>1.75</value></node>
+					<node>single<value>1.47</value></node>
+					<node>aromatic<value>1.39</value></node>
+					<node>double<value>1.34</value></node>
+					<node>triple<value>1.18</value></node>
+					<node>min<value>1.15</value></node>
+				</node>
+			</node>
+			<node>7
+				<node>BondLengths
+					<node>max<value>1.65</value></node>
+					<node>single<value>1.38</value></node>
+					<node>aromatic<value>1.33</value></node>
+					<node>double<value>1.29</value></node>
+					<node>triple<value>1.15</value></node>
+					<node>min<value>1.1</value></node>
+				</node>
+			</node>
+			<node>8
+				<node>BondLengths
+					<node>max<value>1.55</value></node>
+					<node>single<value>1.42</value></node>
+					<node>double<value>1.20</value></node>
+					<node>min<value>1.10</value></node>
+				</node>
+			</node>
+			<node>9
+				<node>BondLengths
+					<node>max<value>1.45</value></node>
+					<node>single<value>1.38</value></node>
+					<node>min<value>1.0</value></node>
+				</node>
+			</node>
+			<node>15
+				<node>BondLengths
+					<node>max<value>1.95</value></node>
+					<node>single<value>1.8</value></node>
+					<node>min<value>1.7</value></node>
+				</node>
+			</node>
+			<node>16
+				<node>BondLengths
+					<node>max<value>1.95</value></node>
+					<node>single<value>1.70</value></node>
+					<node>double<value>1.63</value></node>
+					<node>min<value>1.5</value></node>
+				</node>
+			</node>
+			<node>17
+				<node>BondLengths
+					<node>max<value>1.9</value></node>
+					<node>single<value>1.8</value></node>
+					<node>min<value>1.0</value></node>
+				</node>
+			</node>
+			<node>35
+				<node>BondLengths
+					<node>max<value>2.05</value></node>
+					<node>single<value>1.96</value></node>
+					<node>min<value>1.0</value></node>
+				</node>
+			</node>
+			<node>53
+				<node>BondLengths
+					<node>max<value>2.3</value></node>
+					<node>single<value>2.1</value></node>
+					<node>min<value>1.0</value></node>
+				</node>
+			</node>
+		</node>
+	</node>
+	<node>7
+		<node>Names
+			<node>Nitrogen</node>
+			<node>N</node>
+		</node>
+		<node>Partners
+			<node>7
+				<node>BondLengths
+					<node>max<value>1.55</value></node>
+					<node>single<value>1.40</value></node>
+					<node>aromatic<value>1.32</value></node>
+					<node>double<value>1.22</value></node>
+					<node>min<value>1.0</value></node>
+				</node>
+			</node>
+			<node>8
+				<node>BondLengths
+					<node>max<value>1.5</value></node>
+					<node>single<value>1.4</value></node>
+					<node>double<value>1.21</value></node>
+					<node>min<value>1.15</value></node>
+				</node>
+			</node>
+			<node>9
+				<node>BondLengths
+					<node>max<value>1.5</value></node>
+					<node>single<value>1.35</value></node>
+					<node>min<value>1.25</value></node>
+				</node>
+			</node>
+			<node>15
+				<node>BondLengths
+					<node>max<value>1.8</value></node>
+					<node>single<value>1.68</value></node>
+					<node>aromatic<value>1.60</value></node>
+					<node>double<value>1.58</value></node>
+					<node>min<value>1.5</value></node>
+				</node>
+			</node>
+			<node>16
+				<node>BondLengths
+					<node>max<value>1.80</value></node>
+					<node>single<value>1.65</value></node>
+					<node>aromatic<value>1.56</value></node>
+					<node>double<value>1.54</value></node>
+					<node>min<value>1.50</value></node>
+				</node>
+			</node>
+			<node>17
+				<node>BondLengths
+					<node>max<value>1.85</value></node>
+					<node>single<value>1.74</value></node>
+					<node>min<value>1.65</value></node>
+				</node>
+			</node>
+			<node>35
+				<node>BondLengths
+					<node>max<value>2.0</value></node>
+					<node>single<value>1.84</value></node>
+					<node>min<value>1.7</value></node>
+				</node>
+			</node>
+		</node>
+	</node>
+	<node>8
+		<node>Names
+			<node>Oxygen</node>
+			<node>O</node>
+		</node>
+		<node>Partners
+			<node>8
+				<node>BondLengths
+					<node>max<value>1.55</value></node>
+					<node>single<value>1.47</value></node>
+					<node>min<value>1.40</value></node>
+				</node>
+			</node>
+			<node>15
+				<node>BondLengths
+					<node>max<value>1.75</value></node>
+					<node>single<value>1.59</value></node>
+					<node>double<value>1.49</value></node>
+					<node>min<value>1.40</value></node>
+				</node>
+			</node>
+			<node>16
+				<node>BondLengths
+					<node>max<value>1.75</value></node>
+					<node>single<value>1.56</value></node>
+					<node>double<value>1.43</value></node>
+					<node>min<value>1.38</value></node>
+				</node>
+			</node>
+		</node>
+	</node>
+	<node>15
+		<node>Names
+			<node>Phosphorus</node>
+			<node>P</node>
+		</node>
+		<node>Partners
+			<node>15
+				<node>BondLengths
+					<node>max<value>2.3</value></node>
+					<node>single<value>2.2</value></node>
+					<node>double<value>2.0</value></node>
+					<node>min<value>1.9</value></node>
+				</node>
+			</node>
+			<node>16
+				<node>BondLengths
+					<node>max<value>2.2</value></node>
+					<node>double<value>1.95</value></node>
+					<node>min<value>1.85</value></node>
+				</node>
+			</node>
+		</node>
+	</node>
+	<node>16
+		<node>Names
+			<node>Sulfur</node>
+			<node>S</node>
+		</node>
+		<node>Partners
+			<node>16
+				<node>BondLengths
+					<node>max<value>2.2</value></node>
+					<node>single<value>2.07</value></node>
+					<node>min<value>1.9</value></node>
+				</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/bond_lengths_mmff94.ini	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,1505 @@
+[BondLengths]
+key:I key:deg_I key:J key:deg_J key:order value:r0
+@unit_r0=Angstrom
+;
+;
+;	 I   deg_I   J   deg_J   order      r0
+	--- ------- --- ------- ------- ---------
+	 C     1     C     1       1     1.508
+	 C     1     C     2       1     1.508
+	 C     1     C     3       1     1.508
+	 C     1     C     4       1     1.5086
+	 C     2     C     1       1     1.508
+	 C     2     C     2       1     1.5086
+	 C     2     C     3       1     1.5072
+	 C     2     C     4       1     1.5093
+	 C     3     C     1       1     1.508
+	 C     3     C     2       1     1.5072
+	 C     3     C     3       1     1.5066
+	 C     3     C     4       1     1.51
+	 C     4     C     1       1     1.5086
+	 C     4     C     2       1     1.5093
+	 C     4     C     3       1     1.51
+	 C     4     C     4       1     1.5121
+	 C     1     C     1       2     1.333
+	 C     1     C     2       2     1.333
+	 C     1     C     3       2     1.3333
+	 C     1     C     4       2     1.344
+	 C     2     C     1       2     1.333
+	 C     2     C     2       2     1.3333
+	 C     2     C     3       2     1.3341
+	 C     2     C     4       2     1.3453
+	 C     3     C     1       2     1.3333
+	 C     3     C     2       2     1.3341
+	 C     3     C     3       2     1.3358
+	 C     3     C     4       2     1.3477
+	 C     4     C     1       2     1.344
+	 C     4     C     2       2     1.3453
+	 C     4     C     3       2     1.3477
+	 C     4     C     4       2     1.3624
+	 C     1     C     1       3     1.192
+	 C     1     C     2       3     1.4529
+	 C     1     C     3       3     1.192
+	 C     1     C     4       3     1.1917
+	 C     2     C     1       3     1.452
+	 C     2     C     2       3     1.211
+	 C     2     C     3       3     1.3034
+	 C     2     C     4       3     1.4768
+	 C     3     C     1       3     1.192
+	 C     3     C     2       3     1.299
+	 C     3     C     3       3     1.3358
+	 C     3     C     4       3     1.4835
+	 C     4     C     1       3     1.1917
+	 C     4     C     2       3     1.468
+	 C     4     C     3       3     1.4833
+	 C     4     C     4       3     1.5121
+	 C     1     N     1       1     1.4556
+	 C     1     N     2       1     1.4556
+	 C     1     N     3       1     1.451
+	 C     1     N     4       1     1.4801
+	 C     1     N     5       1     1.5343
+	 C     2     N     1       1     1.4556
+	 C     2     N     3       1     1.4508
+	 C     2     N     4       1     1.4808
+	 C     3     N     1       1     1.4556
+	 C     3     N     3       1     1.4507
+	 C     3     N     4       1     1.4814
+	 C     4     N     1       1     1.4545
+	 C     4     N     3       1     1.452
+	 C     4     N     4       1     1.4757
+	 C     1     N     1       2     1.29
+	 C     1     N     2       2     1.29
+	 C     1     N     3       2     1.28
+	 C     1     N     4       2     1.2913
+	 C     1     N     5       2     1.2904
+	 C     2     N     1       2     1.29
+	 C     2     N     2       2     1.289
+	 C     2     N     3       2     1.2811
+	 C     2     N     4       2     1.2904
+	 C     2     N     5       2     1.2901
+	 C     3     N     1       2     1.2866
+	 C     3     N     2       2     1.2868
+	 C     3     N     3       2     1.2798
+	 C     3     N     4       2     1.2881
+	 C     3     N     5       2     1.2904
+	 C     4     N     1       2     1.3265
+	 C     4     N     2       2     1.3277
+	 C     4     N     3       2     1.29
+	 C     4     N     4       2     1.3347
+	 C     4     N     5       2     1.3364
+	 C     1     N     1       3     1.3756
+	 C     1     N     2       3     1.2075
+	 C     1     N     3       3     1.3756
+	 C     1     N     4       3     1.4018
+	 C     1     N     5       3     1.4163
+	 C     2     N     1       3     1.1897
+	 C     3     N     1       3     1.1154
+	 C     4     N     1       3     1.3758
+	 C     1     O     1       1     1.402
+	 C     1     O     2       1     1.418
+	 C     1     O     3       1     1.402
+	 C     2     O     1       1     1.402
+	 C     2     O     2       1     1.4184
+	 C     2     O     3       1     1.4023
+	 C     3     O     1       1     1.402
+	 C     3     O     2       1     1.4176
+	 C     3     O     3       1     1.4025
+	 C     4     O     1       1     1.3246
+	 C     4     O     2       1     1.4157
+	 C     4     O     3       1     1.4014
+	 C     1     O     1       2     1.222
+	 C     1     O     2       2     1.29
+	 C     1     O     3       2     1.222
+	 C     2     O     1       2     1.222
+	 C     2     O     2       2     1.2905
+	 C     3     O     1       2     1.2246
+	 C     3     O     2       2     1.2928
+	 C     4     O     1       2     1.2649
+	 C     4     O     2       2     1.3136
+	 C     1     O     1       3     1.062
+	 C     1     O     2       3     1.062
+	 C     1     O     3       3     1.062
+	 C     2     O     1       3     1.3947
+	 C     2     O     3       3     1.4092
+	 C     3     O     1       3     1.0599
+	 C     3     O     3       3     1.3525
+	 C     4     O     1       3     1.0617
+	 C     4     O     3       3     1.4161
+	 C     1     P     1       1     1.8346
+	 C     1     P     2       1     1.8347
+	 C     1     P     3       1     1.83
+	 C     1     P     4       1     1.7992
+	 C     1     P     5       1     2.0222
+	 C     1     P     6       1     2.2431
+	 C     2     P     1       1     1.8347
+	 C     2     P     3       1     1.8304
+	 C     2     P     4       1     1.7982
+	 C     3     P     1       1     1.8347
+	 C     3     P     3       1     1.8299
+	 C     3     P     4       1     1.7971
+	 C     4     P     1       1     1.8321
+	 C     4     P     3       1     1.8344
+	 C     4     P     4       1     1.7955
+	 C     1     P     1       2     1.6347
+	 C     1     P     2       2     1.71
+	 C     1     P     3       2     1.6346
+	 C     1     P     4       2     1.6475
+	 C     1     P     5       2     1.6547
+	 C     1     P     6       2     1.6704
+	 C     2     P     1       2     1.6347
+	 C     2     P     2       2     1.7099
+	 C     3     P     1       2     1.6347
+	 C     3     P     2       2     1.7011
+	 C     4     P     1       2     1.6743
+	 C     4     P     2       2     1.7554
+	 C     1     P     1       3     1.4947
+	 C     1     P     2       3     1.4947
+	 C     1     P     3       3     1.4947
+	 C     1     P     4       3     1.5018
+	 C     1     P     5       3     1.5058
+	 C     1     P     6       3     1.5137
+	 C     2     P     1       3     1.7624
+	 C     3     P     1       3     1.4947
+	 C     4     P     1       3     1.494
+	 C     1     S     1       1     1.801
+	 C     1     S     2       1     1.805
+	 C     1     S     3       1     1.805
+	 C     1     S     4       1     1.7882
+	 C     1     S     5       1     1.779
+	 C     1     S     6       1     1.7789
+	 C     2     S     1       1     1.801
+	 C     2     S     2       1     1.8055
+	 C     2     S     3       1     1.805
+	 C     2     S     4       1     1.7875
+	 C     2     S     5       1     1.778
+	 C     2     S     6       1     1.7802
+	 C     3     S     1       1     1.801
+	 C     3     S     2       1     1.8052
+	 C     3     S     3       1     1.8051
+	 C     3     S     4       1     1.7868
+	 C     3     S     5       1     1.777
+	 C     3     S     6       1     1.777
+	 C     4     S     1       1     1.8265
+	 C     4     S     2       1     1.804
+	 C     4     S     3       1     1.8042
+	 C     4     S     4       1     1.786
+	 C     4     S     5       1     1.7765
+	 C     4     S     6       1     1.7805
+	 C     1     S     1       2     1.665
+	 C     1     S     2       2     1.665
+	 C     1     S     3       2     1.665
+	 C     1     S     4       2     1.6803
+	 C     1     S     5       2     1.6889
+	 C     1     S     6       2     1.7087
+	 C     2     S     1       2     1.665
+	 C     3     S     1       2     1.6701
+	 C     4     S     1       2     1.7243
+	 C     1     S     1       3     1.4584
+	 C     1     S     2       3     1.4584
+	 C     1     S     3       3     1.4584
+	 C     1     S     4       3     1.4502
+	 C     1     S     5       3     1.4442
+	 C     1     S     6       3     1.4468
+	 C     2     S     1       3     1.7357
+	 C     2     S     2       3     1.7594
+	 C     2     S     3       3     1.7704
+	 C     2     S     4       3     1.741
+	 C     2     S     5       3     1.7226
+	 C     2     S     6       3     1.7233
+	 C     3     S     1       3     1.7187
+	 C     3     S     2       3     1.7203
+	 C     3     S     3       3     1.7213
+	 C     3     S     4       3     1.6958
+	 C     3     S     5       3     1.6865
+	 C     3     S     6       3     1.6844
+	 C     4     S     1       3     1.8039
+	 C     4     S     2       3     1.804
+	 C     4     S     3       3     1.8042
+	 C     4     S     4       3     1.786
+	 C     4     S     5       3     1.7765
+	 C     4     S     6       3     1.7805
+	 C     1     H     1       1     1.093
+	 C     2     H     1       1     1.093
+	 C     3     H     1       1     1.093
+	 C     4     H     1       1     1.0922
+	 C     1     H     1       2     1.083
+	 C     2     H     1       2     1.083
+	 C     3     H     1       2     1.0826
+	 C     4     H     1       2     1.0922
+	 C     1     H     1       3     1.0907
+	 C     2     H     1       3     1.0701
+	 C     3     H     1       3     1.0826
+	 C     4     H     1       3     1.0922
+	 C     1     Cl     1       1     1.773
+	 C     1     Cl     2       1     1.773
+	 C     1     Cl     3       1     1.773
+	 C     1     Cl     4       1     1.7993
+	 C     2     Cl     1       1     1.773
+	 C     3     Cl     1       1     1.773
+	 C     4     Cl     1       1     1.767
+	 C     1     Cl     1       2     1.72
+	 C     1     Cl     2       2     1.72
+	 C     1     Cl     3       2     1.72
+	 C     1     Cl     4       2     1.7425
+	 C     2     Cl     1       2     1.72
+	 C     3     Cl     1       2     1.7018
+	 C     4     Cl     1       2     1.767
+	 C     1     Cl     1       3     1.4231
+	 C     1     Cl     2       3     1.4231
+	 C     1     Cl     3       3     1.4231
+	 C     1     Cl     4       3     1.4294
+	 C     2     Cl     1       3     1.774
+	 C     3     Cl     1       3     1.7018
+	 C     4     Cl     1       3     1.767
+	 N     1     C     1       1     1.4556
+	 N     1     C     2       1     1.4556
+	 N     1     C     3       1     1.4556
+	 N     1     C     4       1     1.4545
+	 N     2     C     1       1     1.4556
+	 N     3     C     1       1     1.451
+	 N     3     C     2       1     1.4508
+	 N     3     C     3       1     1.4507
+	 N     3     C     4       1     1.452
+	 N     4     C     1       1     1.4801
+	 N     4     C     2       1     1.4808
+	 N     4     C     3       1     1.4814
+	 N     4     C     4       1     1.4757
+	 N     5     C     1       1     1.5343
+	 N     1     C     1       2     1.29
+	 N     1     C     2       2     1.29
+	 N     1     C     3       2     1.2866
+	 N     1     C     4       2     1.3265
+	 N     2     C     1       2     1.29
+	 N     2     C     2       2     1.289
+	 N     2     C     3       2     1.2868
+	 N     2     C     4       2     1.3278
+	 N     3     C     1       2     1.28
+	 N     3     C     2       2     1.2811
+	 N     3     C     3       2     1.2798
+	 N     3     C     4       2     1.29
+	 N     4     C     1       2     1.2913
+	 N     4     C     2       2     1.2904
+	 N     4     C     3       2     1.2881
+	 N     4     C     4       2     1.3347
+	 N     5     C     1       2     1.2904
+	 N     5     C     2       2     1.29
+	 N     5     C     3       2     1.2894
+	 N     5     C     4       2     1.3364
+	 N     1     C     1       3     1.3756
+	 N     1     C     2       3     1.1897
+	 N     1     C     3       3     1.1154
+	 N     1     C     4       3     1.3758
+	 N     2     C     1       3     1.2047
+	 N     3     C     1       3     1.3756
+	 N     4     C     1       3     1.4018
+	 N     5     C     1       3     1.4163
+	 N     1     N     1       1     1.452
+	 N     1     N     2       1     1.452
+	 N     1     N     3       1     1.452
+	 N     1     N     4       1     1.4477
+	 N     1     N     5       1     1.559
+	 N     2     N     1       1     1.452
+	 N     3     N     1       1     1.452
+	 N     3     N     3       1     1.4347
+	 N     3     N     4       1     1.4209
+	 N     4     N     1       1     1.4477
+	 N     4     N     3       1     1.4209
+	 N     4     N     4       1     1.5959
+	 N     5     N     1       1     1.559
+	 N     1     N     1       2     1.243
+	 N     1     N     2       2     1.243
+	 N     1     N     3       2     1.3196
+	 N     1     N     4       2     1.2464
+	 N     1     N     5       2     1.2479
+	 N     2     N     1       2     1.243
+	 N     2     N     2       2     1.2458
+	 N     2     N     3       2     1.3274
+	 N     2     N     4       2     1.2558
+	 N     2     N     5       2     1.262
+	 N     3     N     1       2     1.3196
+	 N     3     N     2       2     1.3274
+	 N     3     N     3       2     1.2614
+	 N     3     N     4       2     1.3566
+	 N     3     N     5       2     1.3758
+	 N     4     N     1       2     1.2464
+	 N     4     N     2       2     1.2558
+	 N     4     N     3       2     1.3565
+	 N     4     N     4       2     1.2902
+	 N     4     N     5       2     1.3128
+	 N     5     N     1       2     1.2479
+	 N     5     N     2       2     1.262
+	 N     5     N     3       2     1.3758
+	 N     5     N     4       2     1.3128
+	 N     5     N     5       2     1.3457
+	 N     1     N     1       3     1.112
+	 N     1     N     2       3     1.1265
+	 N     1     N     3       3     1.112
+	 N     1     N     4       3     1.1212
+	 N     1     N     5       3     1.1263
+	 N     2     N     1       3     1.1265
+	 N     3     N     1       3     1.1121
+	 N     4     N     1       3     1.1212
+	 N     5     N     1       3     1.1263
+	 N     1     O     1       1     1.4175
+	 N     1     O     2       1     1.4175
+	 N     1     O     3       1     1.4175
+	 N     2     O     1       1     1.4175
+	 N     3     O     1       1     1.3875
+	 N     3     O     2       1     1.4537
+	 N     3     O     3       1     1.4468
+	 N     4     O     1       1     1.385
+	 N     4     O     2       1     1.4329
+	 N     4     O     3       1     1.4762
+	 N     5     O     1       1     1.4778
+	 N     1     O     1       2     1.235
+	 N     1     O     2       2     1.2175
+	 N     1     O     3       2     1.235
+	 N     2     O     1       2     1.235
+	 N     3     O     1       2     1.235
+	 N     4     O     1       2     1.2441
+	 N     5     O     1       2     1.2506
+	 N     1     O     1       3     1.3375
+	 N     1     O     2       3     1.3375
+	 N     1     O     3       3     1.3375
+	 N     2     O     1       3     1.4103
+	 N     3     O     1       3     1.3375
+	 N     4     O     1       3     1.3616
+	 N     5     O     1       3     1.376
+	 N     1     P     1       1     1.7389
+	 N     1     P     2       1     1.7389
+	 N     1     P     3       1     1.7389
+	 N     1     P     4       1     1.7303
+	 N     1     P     5       1     1.7713
+	 N     1     P     6       1     1.7981
+	 N     2     P     1       1     1.7389
+	 N     3     P     1       1     1.7389
+	 N     3     P     3       1     1.6998
+	 N     3     P     4       1     1.6531
+	 N     4     P     1       1     1.7339
+	 N     4     P     3       1     1.7493
+	 N     4     P     4       1     1.7184
+	 N     5     P     1       1     1.9769
+	 N     1     P     1       2     1.5389
+	 N     1     P     2       2     1.5389
+	 N     1     P     3       2     1.5389
+	 N     1     P     4       2     1.5479
+	 N     1     P     5       2     1.5531
+	 N     1     P     6       2     1.5625
+	 N     2     P     1       2     1.5389
+	 N     3     P     1       2     1.5389
+	 N     4     P     1       2     1.566
+	 N     5     P     1       2     1.58
+	 N     1     P     1       3     1.6589
+	 N     1     P     2       3     1.6589
+	 N     1     P     3       3     1.6589
+	 N     1     P     4       3     1.6736
+	 N     1     P     5       3     1.6823
+	 N     1     P     6       3     1.7
+	 N     2     P     1       3     1.6808
+	 N     3     P     1       3     1.6589
+	 N     4     P     1       3     1.7072
+	 N     5     P     1       3     1.7778
+	 N     1     S     1       1     1.7181
+	 N     1     S     2       1     1.7181
+	 N     1     S     3       1     1.7181
+	 N     1     S     4       1     1.6908
+	 N     1     S     5       1     1.6742
+	 N     1     S     6       1     1.6812
+	 N     2     S     1       1     1.7181
+	 N     3     S     1       1     1.652
+	 N     3     S     2       1     1.6536
+	 N     3     S     3       1     1.6568
+	 N     3     S     4       1     1.6347
+	 N     3     S     5       1     1.6265
+	 N     3     S     6       1     1.6263
+	 N     4     S     1       1     1.7132
+	 N     4     S     2       1     1.7215
+	 N     4     S     3       1     1.7302
+	 N     4     S     4       1     1.7048
+	 N     4     S     5       1     1.7001
+	 N     4     S     6       1     1.7058
+	 N     5     S     1       1     1.8398
+	 N     1     S     1       2     1.5181
+	 N     1     S     2       2     1.5181
+	 N     1     S     3       2     1.5181
+	 N     1     S     4       2     1.5063
+	 N     1     S     5       2     1.4972
+	 N     1     S     6       2     1.5004
+	 N     2     S     1       2     1.5181
+	 N     3     S     1       2     1.5181
+	 N     3     S     2       2     1.5188
+	 N     3     S     3       2     1.5191
+	 N     3     S     4       2     1.5103
+	 N     3     S     5       2     1.5064
+	 N     3     S     6       2     1.5047
+	 N     4     S     1       2     1.5442
+	 N     5     S     1       2     1.5591
+	 N     1     S     1       3     1.6381
+	 N     1     S     2       3     1.6381
+	 N     1     S     3       3     1.6381
+	 N     1     S     4       3     1.6171
+	 N     1     S     5       3     1.607
+	 N     1     S     6       3     1.6054
+	 N     2     S     1       3     1.7147
+	 N     3     S     1       3     1.6381
+	 N     4     S     1       3     1.6849
+	 N     5     S     1       3     1.7141
+	 N     1     H     1       1     1.0189
+	 N     2     H     1       1     1.0189
+	 N     3     H     1       1     1.019
+	 N     4     H     1       1     1.0268
+	 N     5     H     1       1     1.0449
+	 N     1     H     1       2     1.0189
+	 N     2     H     1       2     1.0189
+	 N     3     H     1       2     1.028
+	 N     4     H     1       2     1.0319
+	 N     5     H     1       2     1.0449
+	 N     1     H     1       3     1.0189
+	 N     2     H     1       3     1.0268
+	 N     3     H     1       3     1.0189
+	 N     4     H     1       3     1.0319
+	 N     5     H     1       3     1.0449
+	 N     1     Cl     1       1     1.7292
+	 N     1     Cl     2       1     1.7291
+	 N     1     Cl     3       1     1.7292
+	 N     1     Cl     4       1     1.7485
+	 N     2     Cl     1       1     1.7292
+	 N     3     Cl     1       1     1.761
+	 N     4     Cl     1       1     1.725
+	 N     5     Cl     1       1     1.8244
+	 N     1     Cl     1       2     1.5292
+	 N     1     Cl     2       2     1.5292
+	 N     1     Cl     3       2     1.5292
+	 N     1     Cl     4       2     1.5376
+	 N     2     Cl     1       2     1.5292
+	 N     3     Cl     1       2     1.5292
+	 N     4     Cl     1       2     1.5515
+	 N     5     Cl     1       2     1.5638
+	 N     1     Cl     1       3     1.6492
+	 N     1     Cl     2       3     1.6492
+	 N     1     Cl     3       3     1.6492
+	 N     1     Cl     4       3     1.6631
+	 N     2     Cl     1       3     1.6958
+	 N     3     Cl     1       3     1.6492
+	 N     4     Cl     1       3     1.6884
+	 N     5     Cl     1       3     1.7114
+	 O     1     C     1       1     1.402
+	 O     1     C     2       1     1.402
+	 O     1     C     3       1     1.402
+	 O     1     C     4       1     1.3246
+	 O     2     C     1       1     1.418
+	 O     2     C     2       1     1.4184
+	 O     2     C     3       1     1.4184
+	 O     2     C     4       1     1.4157
+	 O     3     C     1       1     1.402
+	 O     3     C     2       1     1.4023
+	 O     3     C     3       1     1.4025
+	 O     3     C     4       1     1.4019
+	 O     1     C     1       2     1.222
+	 O     1     C     2       2     1.222
+	 O     1     C     3       2     1.2246
+	 O     1     C     4       2     1.2649
+	 O     2     C     1       2     1.29
+	 O     2     C     2       2     1.2905
+	 O     2     C     3       2     1.2928
+	 O     2     C     4       2     1.3136
+	 O     3     C     1       2     1.222
+	 O     1     C     1       3     1.062
+	 O     1     C     2       3     1.3947
+	 O     1     C     3       3     1.06
+	 O     1     C     4       3     1.0617
+	 O     2     C     1       3     1.062
+	 O     3     C     1       3     1.062
+	 O     3     C     2       3     1.4126
+	 O     3     C     3       3     1.3525
+	 O     3     C     4       3     1.4181
+	 O     1     N     1       1     1.4175
+	 O     1     N     2       1     1.4175
+	 O     1     N     3       1     1.3875
+	 O     1     N     4       1     1.385
+	 O     1     N     5       1     1.4778
+	 O     2     N     1       1     1.4175
+	 O     2     N     3       1     1.4538
+	 O     2     N     4       1     1.4329
+	 O     3     N     1       1     1.4175
+	 O     3     N     3       1     1.4468
+	 O     3     N     4       1     1.4762
+	 O     1     N     1       2     1.235
+	 O     1     N     2       2     1.235
+	 O     1     N     3       2     1.235
+	 O     1     N     4       2     1.2441
+	 O     1     N     5       2     1.2506
+	 O     2     N     1       2     1.2175
+	 O     3     N     1       2     1.235
+	 O     1     N     1       3     1.3375
+	 O     1     N     2       3     1.4103
+	 O     1     N     3       3     1.3374
+	 O     1     N     4       3     1.3616
+	 O     1     N     5       3     1.376
+	 O     2     N     1       3     1.3375
+	 O     3     N     1       3     1.3375
+	 O     1     O     1       1     1.432
+	 O     1     O     2       1     1.432
+	 O     1     O     3       1     1.432
+	 O     2     O     1       1     1.432
+	 O     2     O     2       1     1.4659
+	 O     2     O     3       1     1.4468
+	 O     3     O     1       1     1.432
+	 O     3     O     2       1     1.4468
+	 O     3     O     3       1     1.4631
+	 O     1     O     1       2     1.232
+	 O     1     O     2       2     1.232
+	 O     1     O     3       2     1.232
+	 O     2     O     1       2     1.232
+	 O     2     O     2       2     1.2369
+	 O     2     O     3       2     1.2375
+	 O     3     O     1       2     1.232
+	 O     3     O     2       2     1.2375
+	 O     3     O     3       2     1.4667
+	 O     1     O     1       3     1.092
+	 O     1     O     2       3     1.092
+	 O     1     O     3       3     1.092
+	 O     2     O     1       3     1.092
+	 O     3     O     1       3     1.092
+	 O     3     O     3       3     1.4667
+	 O     1     P     1       1     1.51
+	 O     1     P     2       1     1.51
+	 O     1     P     3       1     1.6467
+	 O     1     P     4       1     1.5102
+	 O     1     P     5       1     1.5119
+	 O     1     P     6       1     1.5149
+	 O     2     P     1       1     1.63
+	 O     2     P     2       1     1.6298
+	 O     2     P     3       1     1.6192
+	 O     2     P     4       1     1.6219
+	 O     2     P     5       1     1.6147
+	 O     2     P     6       1     1.6169
+	 O     3     P     1       1     1.6767
+	 O     3     P     2       1     1.6765
+	 O     3     P     3       1     1.6799
+	 O     3     P     4       1     1.6668
+	 O     3     P     5       1     1.6617
+	 O     3     P     6       1     1.6635
+	 O     1     P     1       2     1.4767
+	 O     1     P     2       2     1.4767
+	 O     1     P     3       2     1.4767
+	 O     1     P     4       2     1.474
+	 O     1     P     5       2     1.4732
+	 O     1     P     6       2     1.4742
+	 O     2     P     1       2     1.4767
+	 O     2     P     2       2     1.4766
+	 O     2     P     3       2     1.476
+	 O     2     P     4       2     1.4729
+	 O     2     P     5       2     1.4709
+	 O     2     P     6       2     1.4712
+	 O     3     P     1       2     1.63
+	 O     3     P     2       2     1.6298
+	 O     3     P     3       2     1.6293
+	 O     3     P     4       2     1.6213
+	 O     3     P     5       2     1.6135
+	 O     3     P     6       2     1.6154
+	 O     1     P     1       3     1.3367
+	 O     1     P     2       3     1.3367
+	 O     1     P     3       3     1.3367
+	 O     1     P     4       3     1.3349
+	 O     1     P     5       3     1.334
+	 O     1     P     6       3     1.3342
+	 O     2     P     1       3     1.3367
+	 O     3     P     1       3     1.63
+	 O     3     P     2       3     1.6298
+	 O     3     P     3       3     1.6293
+	 O     3     P     4       3     1.6213
+	 O     3     P     5       3     1.6135
+	 O     3     P     6       3     1.6154
+	 O     1     S     1       1     1.6632
+	 O     1     S     2       1     1.6632
+	 O     1     S     3       1     1.661
+	 O     1     S     4       1     1.6179
+	 O     1     S     5       1     1.6344
+	 O     1     S     6       1     1.633
+	 O     2     S     1       1     1.661
+	 O     2     S     2       1     1.6636
+	 O     2     S     3       1     1.6638
+	 O     2     S     4       1     1.6478
+	 O     2     S     5       1     1.6402
+	 O     2     S     6       1     1.6398
+	 O     3     S     1       1     1.6632
+	 O     3     S     2       1     1.6606
+	 O     3     S     3       1     1.6738
+	 O     3     S     4       1     1.6549
+	 O     3     S     5       1     1.6498
+	 O     3     S     6       1     1.6489
+	 O     1     S     1       2     1.5
+	 O     1     S     2       2     1.5
+	 O     1     S     3       2     1.5
+	 O     1     S     4       2     1.5008
+	 O     1     S     5       2     1.503
+	 O     1     S     6       2     1.5062
+	 O     2     S     1       2     1.4632
+	 O     3     S     1       2     1.5
+	 O     1     S     1       3     1.3232
+	 O     1     S     2       3     1.3232
+	 O     1     S     3       3     1.3232
+	 O     1     S     4       3     1.3194
+	 O     1     S     5       3     1.3167
+	 O     1     S     6       3     1.3164
+	 O     2     S     1       3     1.3232
+	 O     2     S     3       3     1.6638
+	 O     2     S     4       3     1.6478
+	 O     2     S     5       3     1.6402
+	 O     2     S     6       3     1.6398
+	 O     3     S     1       3     1.661
+	 O     3     S     2       3     1.6593
+	 O     3     S     3       3     1.6685
+	 O     3     S     4       3     1.6505
+	 O     3     S     5       3     1.6437
+	 O     3     S     6       3     1.6421
+	 O     1     H     1       1     0.97781
+	 O     2     H     1       1     0.969
+	 O     3     H     1       1     0.991
+	 O     1     H     1       2     0.97781
+	 O     2     H     1       2     0.987
+	 O     3     H     1       2     0.97781
+	 O     1     H     1       3     0.991
+	 O     2     H     1       3     0.97781
+	 O     3     H     1       3     0.97781
+	 O     1     Cl     1       1     1.6843
+	 O     1     Cl     2       1     1.6843
+	 O     1     Cl     3       1     1.6843
+	 O     1     Cl     4       1     1.6998
+	 O     2     Cl     1       1     1.6843
+	 O     3     Cl     1       1     1.6843
+	 O     1     Cl     1       2     1.4843
+	 O     1     Cl     2       2     1.4843
+	 O     1     Cl     3       2     1.4843
+	 O     1     Cl     4       2     1.491
+	 O     2     Cl     1       2     1.4843
+	 O     3     Cl     1       2     1.4843
+	 O     1     Cl     1       3     1.3443
+	 O     1     Cl     2       3     1.3443
+	 O     1     Cl     3       3     1.3443
+	 O     1     Cl     4       3     1.3479
+	 O     2     Cl     1       3     1.3443
+	 O     3     Cl     1       3     1.3443
+	 P     1     C     1       1     1.8346
+	 P     1     C     2       1     1.8347
+	 P     1     C     3       1     1.8347
+	 P     1     C     4       1     1.8321
+	 P     2     C     1       1     1.8347
+	 P     3     C     1       1     1.83
+	 P     3     C     2       1     1.8299
+	 P     3     C     3       1     1.8299
+	 P     3     C     4       1     1.8344
+	 P     4     C     1       1     1.7992
+	 P     4     C     2       1     1.7982
+	 P     4     C     3       1     1.7971
+	 P     4     C     4       1     1.7955
+	 P     5     C     1       1     2.0222
+	 P     6     C     1       1     2.2431
+	 P     1     C     1       2     1.6347
+	 P     1     C     2       2     1.6347
+	 P     1     C     3       2     1.6346
+	 P     1     C     4       2     1.6743
+	 P     2     C     1       2     1.71
+	 P     2     C     2       2     1.7099
+	 P     2     C     3       2     1.7011
+	 P     2     C     4       2     1.7571
+	 P     3     C     1       2     1.6347
+	 P     4     C     1       2     1.6475
+	 P     5     C     1       2     1.6547
+	 P     6     C     1       2     1.6704
+	 P     1     C     1       3     1.4947
+	 P     1     C     2       3     1.7548
+	 P     1     C     3       3     1.4947
+	 P     1     C     4       3     1.494
+	 P     2     C     1       3     1.4947
+	 P     3     C     1       3     1.4947
+	 P     4     C     1       3     1.5018
+	 P     5     C     1       3     1.5058
+	 P     6     C     1       3     1.5137
+	 P     1     N     1       1     1.7389
+	 P     1     N     2       1     1.7389
+	 P     1     N     3       1     1.7389
+	 P     1     N     4       1     1.7339
+	 P     1     N     5       1     1.9769
+	 P     2     N     1       1     1.7389
+	 P     3     N     1       1     1.7389
+	 P     3     N     3       1     1.6998
+	 P     3     N     4       1     1.7493
+	 P     4     N     1       1     1.7303
+	 P     4     N     3       1     1.6508
+	 P     4     N     4       1     1.7184
+	 P     5     N     1       1     1.7713
+	 P     6     N     1       1     1.7981
+	 P     1     N     1       2     1.5389
+	 P     1     N     2       2     1.5389
+	 P     1     N     3       2     1.5389
+	 P     1     N     4       2     1.566
+	 P     1     N     5       2     1.58
+	 P     2     N     1       2     1.5389
+	 P     3     N     1       2     1.5389
+	 P     4     N     1       2     1.5479
+	 P     5     N     1       2     1.5531
+	 P     6     N     1       2     1.5625
+	 P     1     N     1       3     1.6589
+	 P     1     N     2       3     1.6808
+	 P     1     N     3       3     1.6589
+	 P     1     N     4       3     1.7072
+	 P     1     N     5       3     1.7778
+	 P     2     N     1       3     1.6589
+	 P     3     N     1       3     1.6589
+	 P     4     N     1       3     1.6736
+	 P     5     N     1       3     1.6823
+	 P     6     N     1       3     1.7
+	 P     1     O     1       1     1.51
+	 P     1     O     2       1     1.63
+	 P     1     O     3       1     1.6767
+	 P     2     O     1       1     1.51
+	 P     2     O     2       1     1.6298
+	 P     2     O     3       1     1.6765
+	 P     3     O     1       1     1.6467
+	 P     3     O     2       1     1.6194
+	 P     3     O     3       1     1.6799
+	 P     4     O     1       1     1.5102
+	 P     4     O     2       1     1.6219
+	 P     4     O     3       1     1.6664
+	 P     5     O     1       1     1.5119
+	 P     5     O     2       1     1.6147
+	 P     5     O     3       1     1.6617
+	 P     6     O     1       1     1.5148
+	 P     6     O     2       1     1.617
+	 P     6     O     3       1     1.6635
+	 P     1     O     1       2     1.4767
+	 P     1     O     2       2     1.4767
+	 P     1     O     3       2     1.63
+	 P     2     O     1       2     1.4767
+	 P     2     O     2       2     1.4766
+	 P     2     O     3       2     1.6298
+	 P     3     O     1       2     1.4767
+	 P     3     O     2       2     1.476
+	 P     3     O     3       2     1.6293
+	 P     4     O     1       2     1.474
+	 P     4     O     2       2     1.4728
+	 P     4     O     3       2     1.6213
+	 P     5     O     1       2     1.4732
+	 P     5     O     2       2     1.4706
+	 P     5     O     3       2     1.6134
+	 P     6     O     1       2     1.4741
+	 P     6     O     2       2     1.4719
+	 P     6     O     3       2     1.6153
+	 P     1     O     1       3     1.3367
+	 P     1     O     2       3     1.3367
+	 P     1     O     3       3     1.63
+	 P     2     O     1       3     1.3367
+	 P     2     O     3       3     1.6298
+	 P     3     O     1       3     1.3367
+	 P     3     O     3       3     1.6293
+	 P     4     O     1       3     1.3349
+	 P     4     O     3       3     1.6213
+	 P     5     O     1       3     1.334
+	 P     5     O     3       3     1.6134
+	 P     6     O     1       3     1.3342
+	 P     6     O     3       3     1.6153
+	 P     1     P     1       1     2.18
+	 P     1     P     2       1     2.18
+	 P     1     P     3       1     2.18
+	 P     1     P     4       1     2.1607
+	 P     1     P     5       1     2.2615
+	 P     1     P     6       1     2.3913
+	 P     2     P     1       1     2.18
+	 P     3     P     1       1     2.18
+	 P     3     P     3       1     2.2788
+	 P     3     P     4       1     2.1532
+	 P     4     P     1       1     2.1607
+	 P     4     P     3       1     2.1532
+	 P     4     P     4       1     2.1946
+	 P     5     P     1       1     2.2616
+	 P     6     P     1       1     2.3913
+	 P     1     P     1       2     1.98
+	 P     1     P     2       2     1.98
+	 P     1     P     3       2     1.98
+	 P     1     P     4       2     2.0047
+	 P     1     P     5       2     2.0183
+	 P     1     P     6       2     2.0574
+	 P     2     P     1       2     1.98
+	 P     3     P     1       2     1.9801
+	 P     4     P     1       2     2.0047
+	 P     5     P     1       2     2.0183
+	 P     6     P     1       2     2.0574
+	 P     1     P     1       3     1.84
+	 P     1     P     2       3     1.84
+	 P     1     P     3       3     1.84
+	 P     1     P     4       3     1.8549
+	 P     1     P     5       3     1.8629
+	 P     1     P     6       3     1.8829
+	 P     2     P     1       3     1.84
+	 P     3     P     1       3     1.84
+	 P     4     P     1       3     1.8549
+	 P     5     P     1       3     1.8629
+	 P     6     P     1       3     1.8829
+	 P     1     S     1       1     2.0694
+	 P     1     S     2       1     2.0994
+	 P     1     S     3       1     2.0994
+	 P     1     S     4       1     2.0512
+	 P     1     S     5       1     2.0582
+	 P     1     S     6       1     2.0526
+	 P     2     S     1       1     2.0694
+	 P     3     S     1       1     2.0694
+	 P     3     S     2       1     2.107
+	 P     3     S     3       1     2.1076
+	 P     3     S     4       1     2.0602
+	 P     3     S     5       1     2.0668
+	 P     3     S     6       1     2.0404
+	 P     4     S     1       1     1.9399
+	 P     4     S     2       1     2.0942
+	 P     4     S     3       1     2.0932
+	 P     4     S     4       1     2.0484
+	 P     4     S     5       1     2.0344
+	 P     4     S     6       1     2.0272
+	 P     5     S     1       1     2.1158
+	 P     6     S     1       1     2.1603
+	 P     1     S     1       2     1.8994
+	 P     1     S     2       2     1.8994
+	 P     1     S     3       2     1.8994
+	 P     1     S     4       2     1.8737
+	 P     1     S     5       2     1.8769
+	 P     1     S     6       2     1.8723
+	 P     2     S     1       2     1.8994
+	 P     3     S     1       2     1.8994
+	 P     4     S     1       2     1.9151
+	 P     5     S     1       2     1.9244
+	 P     6     S     1       2     1.9437
+	 P     1     S     1       3     1.7594
+	 P     1     S     2       3     1.7594
+	 P     1     S     3       3     1.7594
+	 P     1     S     4       3     1.7438
+	 P     1     S     5       3     1.7452
+	 P     1     S     6       3     1.7418
+	 P     2     S     1       3     1.7594
+	 P     3     S     1       3     1.7594
+	 P     4     S     1       3     1.7688
+	 P     5     S     1       3     1.7743
+	 P     6     S     1       3     1.7843
+	 P     1     H     1       1     1.4168
+	 P     2     H     1       1     1.4168
+	 P     3     H     1       1     1.415
+	 P     4     H     1       1     1.411
+	 P     5     H     1       1     1.4168
+	 P     6     H     1       1     1.4168
+	 P     1     H     1       2     1.4168
+	 P     2     H     1       2     1.4168
+	 P     3     H     1       2     1.4168
+	 P     4     H     1       2     1.4168
+	 P     5     H     1       2     1.4168
+	 P     6     H     1       2     1.4168
+	 P     1     H     1       3     1.4168
+	 P     2     H     1       3     1.4168
+	 P     3     H     1       3     1.4168
+	 P     4     H     1       3     1.4168
+	 P     5     H     1       3     1.4168
+	 P     6     H     1       3     1.4168
+	 P     1     Cl     1       1     2.0445
+	 P     1     Cl     2       1     2.0445
+	 P     1     Cl     3       1     2.0445
+	 P     1     Cl     4       1     2.0745
+	 P     2     Cl     1       1     2.0445
+	 P     3     Cl     1       1     2.1
+	 P     4     Cl     1       1     2.0103
+	 P     5     Cl     1       1     2.0863
+	 P     6     Cl     1       1     2.1254
+	 P     1     Cl     1       2     1.8445
+	 P     1     Cl     2       2     1.8445
+	 P     1     Cl     3       2     1.8445
+	 P     1     Cl     4       2     1.8591
+	 P     2     Cl     1       2     1.8445
+	 P     3     Cl     1       2     1.8445
+	 P     4     Cl     1       2     1.8573
+	 P     5     Cl     1       2     1.8648
+	 P     6     Cl     1       2     1.8799
+	 P     1     Cl     1       3     1.7045
+	 P     1     Cl     2       3     1.7045
+	 P     1     Cl     3       3     1.7044
+	 P     1     Cl     4       3     1.7132
+	 P     2     Cl     1       3     1.7045
+	 P     3     Cl     1       3     1.7046
+	 P     4     Cl     1       3     1.7121
+	 P     5     Cl     1       3     1.7165
+	 P     6     Cl     1       3     1.7244
+	 S     1     C     1       1     1.801
+	 S     1     C     2       1     1.801
+	 S     1     C     3       1     1.801
+	 S     1     C     4       1     1.8265
+	 S     2     C     1       1     1.805
+	 S     2     C     2       1     1.8055
+	 S     2     C     3       1     1.8052
+	 S     2     C     4       1     1.804
+	 S     3     C     1       1     1.805
+	 S     3     C     2       1     1.8053
+	 S     3     C     3       1     1.8052
+	 S     3     C     4       1     1.8042
+	 S     4     C     1       1     1.7882
+	 S     4     C     2       1     1.7875
+	 S     4     C     3       1     1.7868
+	 S     4     C     4       1     1.786
+	 S     5     C     1       1     1.779
+	 S     5     C     2       1     1.7781
+	 S     5     C     3       1     1.777
+	 S     5     C     4       1     1.7765
+	 S     6     C     1       1     1.7815
+	 S     6     C     2       1     1.78
+	 S     6     C     3       1     1.7812
+	 S     6     C     4       1     1.7808
+	 S     1     C     1       2     1.665
+	 S     1     C     2       2     1.665
+	 S     1     C     3       2     1.6701
+	 S     1     C     4       2     1.7243
+	 S     2     C     1       2     1.665
+	 S     3     C     1       2     1.665
+	 S     4     C     1       2     1.6803
+	 S     5     C     1       2     1.6889
+	 S     6     C     1       2     1.7086
+	 S     1     C     1       3     1.4584
+	 S     1     C     2       3     1.7389
+	 S     1     C     3       3     1.7187
+	 S     1     C     4       3     1.8039
+	 S     2     C     1       3     1.4584
+	 S     2     C     2       3     1.7594
+	 S     2     C     3       3     1.7203
+	 S     2     C     4       3     1.804
+	 S     3     C     1       3     1.4584
+	 S     3     C     2       3     1.7586
+	 S     3     C     3       3     1.7213
+	 S     3     C     4       3     1.8042
+	 S     4     C     1       3     1.4502
+	 S     4     C     2       3     1.737
+	 S     4     C     3       3     1.6958
+	 S     4     C     4       3     1.786
+	 S     5     C     1       3     1.4442
+	 S     5     C     2       3     1.7251
+	 S     5     C     3       3     1.6865
+	 S     5     C     4       3     1.7765
+	 S     6     C     1       3     1.4468
+	 S     6     C     2       3     1.7195
+	 S     6     C     3       3     1.6847
+	 S     6     C     4       3     1.7808
+	 S     1     N     1       1     1.7181
+	 S     1     N     2       1     1.7181
+	 S     1     N     3       1     1.652
+	 S     1     N     4       1     1.7132
+	 S     1     N     5       1     1.8397
+	 S     2     N     1       1     1.7181
+	 S     2     N     3       1     1.6536
+	 S     2     N     4       1     1.7215
+	 S     3     N     1       1     1.7181
+	 S     3     N     3       1     1.6568
+	 S     3     N     4       1     1.7302
+	 S     4     N     1       1     1.6908
+	 S     4     N     3       1     1.6347
+	 S     4     N     4       1     1.7048
+	 S     5     N     1       1     1.6742
+	 S     5     N     3       1     1.626
+	 S     5     N     4       1     1.7001
+	 S     6     N     1       1     1.6812
+	 S     6     N     3       1     1.6271
+	 S     6     N     4       1     1.7058
+	 S     1     N     1       2     1.5181
+	 S     1     N     2       2     1.5181
+	 S     1     N     3       2     1.5181
+	 S     1     N     4       2     1.5442
+	 S     1     N     5       2     1.5591
+	 S     2     N     1       2     1.5181
+	 S     2     N     3       2     1.5188
+	 S     3     N     1       2     1.5181
+	 S     3     N     3       2     1.5191
+	 S     4     N     1       2     1.5063
+	 S     4     N     3       2     1.5102
+	 S     5     N     1       2     1.4972
+	 S     5     N     3       2     1.5058
+	 S     6     N     1       2     1.5003
+	 S     6     N     3       2     1.5046
+	 S     1     N     1       3     1.6381
+	 S     1     N     2       3     1.7093
+	 S     1     N     3       3     1.6381
+	 S     1     N     4       3     1.6849
+	 S     1     N     5       3     1.7141
+	 S     2     N     1       3     1.6381
+	 S     3     N     1       3     1.6381
+	 S     4     N     1       3     1.6171
+	 S     5     N     1       3     1.607
+	 S     6     N     1       3     1.6054
+	 S     1     O     1       1     1.6632
+	 S     1     O     2       1     1.661
+	 S     1     O     3       1     1.6632
+	 S     2     O     1       1     1.6632
+	 S     2     O     2       1     1.6636
+	 S     2     O     3       1     1.6606
+	 S     3     O     1       1     1.661
+	 S     3     O     2       1     1.6638
+	 S     3     O     3       1     1.6738
+	 S     4     O     1       1     1.6179
+	 S     4     O     2       1     1.6478
+	 S     4     O     3       1     1.6549
+	 S     5     O     1       1     1.6344
+	 S     5     O     2       1     1.6399
+	 S     5     O     3       1     1.6498
+	 S     6     O     1       1     1.6331
+	 S     6     O     2       1     1.6397
+	 S     6     O     3       1     1.6488
+	 S     1     O     1       2     1.5
+	 S     1     O     2       2     1.4632
+	 S     1     O     3       2     1.5
+	 S     2     O     1       2     1.5
+	 S     3     O     1       2     1.5
+	 S     4     O     1       2     1.5008
+	 S     5     O     1       2     1.503
+	 S     6     O     1       2     1.5062
+	 S     1     O     1       3     1.3232
+	 S     1     O     2       3     1.3232
+	 S     1     O     3       3     1.661
+	 S     2     O     1       3     1.3232
+	 S     2     O     3       3     1.6592
+	 S     3     O     1       3     1.3232
+	 S     3     O     2       3     1.6638
+	 S     3     O     3       3     1.6685
+	 S     4     O     1       3     1.3194
+	 S     4     O     2       3     1.6478
+	 S     4     O     3       3     1.65
+	 S     5     O     1       3     1.3167
+	 S     5     O     2       3     1.6399
+	 S     5     O     3       3     1.6437
+	 S     6     O     1       3     1.3163
+	 S     6     O     2       3     1.6397
+	 S     6     O     3       3     1.6422
+	 S     1     P     1       1     2.0694
+	 S     1     P     2       1     2.0694
+	 S     1     P     3       1     2.0694
+	 S     1     P     4       1     1.94
+	 S     1     P     5       1     2.1158
+	 S     1     P     6       1     2.1603
+	 S     2     P     1       1     2.0994
+	 S     2     P     3       1     2.107
+	 S     2     P     4       1     2.0942
+	 S     3     P     1       1     2.0994
+	 S     3     P     3       1     2.1076
+	 S     3     P     4       1     2.0932
+	 S     4     P     1       1     2.0924
+	 S     4     P     3       1     2.0602
+	 S     4     P     4       1     2.0484
+	 S     5     P     1       1     2.0582
+	 S     5     P     3       1     2.0471
+	 S     5     P     4       1     2.0344
+	 S     6     P     1       1     2.0526
+	 S     6     P     3       1     2.0396
+	 S     6     P     4       1     2.0263
+	 S     1     P     1       2     1.8994
+	 S     1     P     2       2     1.8994
+	 S     1     P     3       2     1.8994
+	 S     1     P     4       2     1.9151
+	 S     1     P     5       2     1.9244
+	 S     1     P     6       2     1.9437
+	 S     2     P     1       2     1.8994
+	 S     3     P     1       2     1.8994
+	 S     4     P     1       2     1.8737
+	 S     5     P     1       2     1.8624
+	 S     6     P     1       2     1.8723
+	 S     1     P     1       3     1.7594
+	 S     1     P     2       3     1.7594
+	 S     1     P     3       3     1.7595
+	 S     1     P     4       3     1.7688
+	 S     1     P     5       3     1.7743
+	 S     1     P     6       3     1.7843
+	 S     2     P     1       3     1.7594
+	 S     3     P     1       3     1.7594
+	 S     4     P     1       3     1.7438
+	 S     5     P     1       3     1.7359
+	 S     6     P     1       3     1.7418
+	 S     1     S     1       1     2.05
+	 S     1     S     2       1     2.05
+	 S     1     S     3       1     2.05
+	 S     1     S     4       1     2.007
+	 S     1     S     5       1     1.9923
+	 S     1     S     6       1     1.9875
+	 S     2     S     1       1     2.05
+	 S     2     S     2       1     2.0515
+	 S     2     S     3       1     2.0496
+	 S     2     S     4       1     2.0082
+	 S     2     S     5       1     1.9947
+	 S     2     S     6       1     1.9865
+	 S     3     S     1       1     2.05
+	 S     3     S     2       1     2.0496
+	 S     3     S     3       1     2.0528
+	 S     3     S     4       1     2.0097
+	 S     3     S     5       1     1.9973
+	 S     3     S     6       1     1.9924
+	 S     4     S     1       1     2.007
+	 S     4     S     2       1     2.0082
+	 S     4     S     3       1     2.0097
+	 S     4     S     4       1     1.9769
+	 S     4     S     5       1     1.9671
+	 S     4     S     6       1     1.9605
+	 S     5     S     1       1     1.9923
+	 S     5     S     2       1     1.9947
+	 S     5     S     3       1     1.9972
+	 S     5     S     4       1     1.9671
+	 S     5     S     5       1     1.9587
+	 S     5     S     6       1     1.9559
+	 S     6     S     1       1     1.9875
+	 S     6     S     2       1     1.9866
+	 S     6     S     3       1     1.9924
+	 S     6     S     4       1     1.9606
+	 S     6     S     5       1     1.9566
+	 S     6     S     6       1     1.9493
+	 S     1     S     1       2     2.05
+	 S     1     S     2       2     2.05
+	 S     1     S     3       2     2.05
+	 S     1     S     4       2     2.007
+	 S     1     S     5       2     1.9923
+	 S     1     S     6       2     1.9875
+	 S     2     S     1       2     2.05
+	 S     2     S     2       2     2.0515
+	 S     2     S     3       2     2.0496
+	 S     2     S     4       2     2.0082
+	 S     2     S     5       2     1.9947
+	 S     2     S     6       2     1.9865
+	 S     3     S     1       2     2.05
+	 S     3     S     2       2     2.0496
+	 S     3     S     3       2     2.0528
+	 S     3     S     4       2     2.0097
+	 S     3     S     5       2     1.9973
+	 S     3     S     6       2     1.9924
+	 S     4     S     1       2     2.007
+	 S     4     S     2       2     2.0082
+	 S     4     S     3       2     2.0097
+	 S     4     S     4       2     1.9769
+	 S     4     S     5       2     1.9671
+	 S     4     S     6       2     1.9605
+	 S     5     S     1       2     1.9923
+	 S     5     S     2       2     1.9947
+	 S     5     S     3       2     1.9972
+	 S     5     S     4       2     1.9671
+	 S     5     S     5       2     1.9587
+	 S     5     S     6       2     1.9559
+	 S     6     S     1       2     1.9875
+	 S     6     S     2       2     1.9866
+	 S     6     S     3       2     1.9924
+	 S     6     S     4       2     1.9606
+	 S     6     S     5       2     1.9566
+	 S     6     S     6       2     1.9493
+	 S     1     S     1       3     2.05
+	 S     1     S     2       3     2.05
+	 S     1     S     3       3     2.05
+	 S     1     S     4       3     2.007
+	 S     1     S     5       3     1.9923
+	 S     1     S     6       3     1.9875
+	 S     2     S     1       3     2.05
+	 S     2     S     2       3     2.0515
+	 S     2     S     3       3     2.0496
+	 S     2     S     4       3     2.0082
+	 S     2     S     5       3     1.9947
+	 S     2     S     6       3     1.9865
+	 S     3     S     1       3     2.05
+	 S     3     S     2       3     2.0496
+	 S     3     S     3       3     2.0528
+	 S     3     S     4       3     2.0097
+	 S     3     S     5       3     1.9973
+	 S     3     S     6       3     1.9924
+	 S     4     S     1       3     2.007
+	 S     4     S     2       3     2.0082
+	 S     4     S     3       3     2.0097
+	 S     4     S     4       3     1.9769
+	 S     4     S     5       3     1.9671
+	 S     4     S     6       3     1.9605
+	 S     5     S     1       3     1.9923
+	 S     5     S     2       3     1.9947
+	 S     5     S     3       3     1.9972
+	 S     5     S     4       3     1.9671
+	 S     5     S     5       3     1.9587
+	 S     5     S     6       3     1.9559
+	 S     6     S     1       3     1.9875
+	 S     6     S     2       3     1.9866
+	 S     6     S     3       3     1.9924
+	 S     6     S     4       3     1.9606
+	 S     6     S     5       3     1.9566
+	 S     6     S     6       3     1.9493
+	 S     1     H     1       1     1.341
+	 S     2     H     1       1     1.341
+	 S     3     H     1       1     1.341
+	 S     4     H     1       1     1.3318
+	 S     5     H     1       1     1.3272
+	 S     6     H     1       1     1.3317
+	 S     1     H     1       2     1.341
+	 S     2     H     1       2     1.341
+	 S     3     H     1       2     1.341
+	 S     4     H     1       2     1.3318
+	 S     5     H     1       2     1.3272
+	 S     6     H     1       2     1.3317
+	 S     1     H     1       3     1.341
+	 S     2     H     1       3     1.341
+	 S     3     H     1       3     1.341
+	 S     4     H     1       3     1.3318
+	 S     5     H     1       3     1.3272
+	 S     6     H     1       3     1.3317
+	 S     1     Cl     1       1     2.031
+	 S     1     Cl     2       1     2.031
+	 S     1     Cl     3       1     2.031
+	 S     1     Cl     4       1     2.0566
+	 S     2     Cl     1       1     2.031
+	 S     3     Cl     1       1     2.031
+	 S     4     Cl     1       1     1.9985
+	 S     5     Cl     1       1     1.9855
+	 S     6     Cl     1       1     1.9827
+	 S     1     Cl     1       2     2.031
+	 S     1     Cl     2       2     2.031
+	 S     1     Cl     3       2     2.031
+	 S     1     Cl     4       2     2.0566
+	 S     2     Cl     1       2     2.031
+	 S     3     Cl     1       2     2.031
+	 S     4     Cl     1       2     1.9985
+	 S     5     Cl     1       2     1.9855
+	 S     6     Cl     1       2     1.9827
+	 S     1     Cl     1       3     2.031
+	 S     1     Cl     2       3     2.031
+	 S     1     Cl     3       3     2.031
+	 S     1     Cl     4       3     2.0566
+	 S     2     Cl     1       3     2.031
+	 S     3     Cl     1       3     2.031
+	 S     4     Cl     1       3     1.9985
+	 S     5     Cl     1       3     1.9855
+	 S     6     Cl     1       3     1.9827
+	 H     1     C     1       1     1.093
+	 H     1     C     2       1     1.093
+	 H     1     C     3       1     1.093
+	 H     1     C     4       1     1.0922
+	 H     1     C     1       2     1.083
+	 H     1     C     2       2     1.083
+	 H     1     C     3       2     1.0826
+	 H     1     C     4       2     1.0922
+	 H     1     C     1       3     1.0907
+	 H     1     C     2       3     1.0701
+	 H     1     C     3       3     1.0826
+	 H     1     C     4       3     1.0922
+	 H     1     N     1       1     1.0189
+	 H     1     N     2       1     1.0189
+	 H     1     N     3       1     1.019
+	 H     1     N     4       1     1.0268
+	 H     1     N     5       1     1.0449
+	 H     1     N     1       2     1.0189
+	 H     1     N     2       2     1.0189
+	 H     1     N     3       2     1.028
+	 H     1     N     4       2     1.0319
+	 H     1     N     5       2     1.0449
+	 H     1     N     1       3     1.0189
+	 H     1     N     2       3     1.0268
+	 H     1     N     3       3     1.0189
+	 H     1     N     4       3     1.0319
+	 H     1     N     5       3     1.0449
+	 H     1     O     1       1     0.97781
+	 H     1     O     2       1     0.969
+	 H     1     O     3       1     0.991
+	 H     1     O     1       2     0.97781
+	 H     1     O     2       2     0.987
+	 H     1     O     3       2     0.97784
+	 H     1     O     1       3     0.991
+	 H     1     O     2       3     0.97781
+	 H     1     O     3       3     0.97784
+	 H     1     P     1       1     1.4168
+	 H     1     P     2       1     1.4168
+	 H     1     P     3       1     1.415
+	 H     1     P     4       1     1.411
+	 H     1     P     5       1     1.4168
+	 H     1     P     6       1     1.4168
+	 H     1     P     1       2     1.4168
+	 H     1     P     2       2     1.4168
+	 H     1     P     3       2     1.4168
+	 H     1     P     4       2     1.4168
+	 H     1     P     5       2     1.4168
+	 H     1     P     6       2     1.4168
+	 H     1     P     1       3     1.4168
+	 H     1     P     2       3     1.4168
+	 H     1     P     3       3     1.4168
+	 H     1     P     4       3     1.4168
+	 H     1     P     5       3     1.4168
+	 H     1     P     6       3     1.4168
+	 H     1     S     1       1     1.341
+	 H     1     S     2       1     1.341
+	 H     1     S     3       1     1.341
+	 H     1     S     4       1     1.3318
+	 H     1     S     5       1     1.3335
+	 H     1     S     6       1     1.3317
+	 H     1     S     1       2     1.341
+	 H     1     S     2       2     1.341
+	 H     1     S     3       2     1.341
+	 H     1     S     4       2     1.3318
+	 H     1     S     5       2     1.3335
+	 H     1     S     6       2     1.3317
+	 H     1     S     1       3     1.341
+	 H     1     S     2       3     1.341
+	 H     1     S     3       3     1.341
+	 H     1     S     4       3     1.3318
+	 H     1     S     5       3     1.3335
+	 H     1     S     6       3     1.3317
+	 H     1     H     1       1     0.66
+	 H     1     H     1       2     0.66
+	 H     1     H     1       3     0.66
+	 H     1     Cl     1       1     1.3138
+	 H     1     Cl     2       1     1.3138
+	 H     1     Cl     3       1     1.3138
+	 H     1     Cl     4       1     1.3138
+	 H     1     Cl     1       2     1.3138
+	 H     1     Cl     2       2     1.3138
+	 H     1     Cl     3       2     1.3138
+	 H     1     Cl     4       2     1.3138
+	 H     1     Cl     1       3     1.3138
+	 H     1     Cl     2       3     1.3138
+	 H     1     Cl     3       3     1.3138
+	 H     1     Cl     4       3     1.3138
+	 Cl     1     C     1       1     1.773
+	 Cl     1     C     2       1     1.773
+	 Cl     1     C     3       1     1.773
+	 Cl     1     C     4       1     1.767
+	 Cl     2     C     1       1     1.773
+	 Cl     3     C     1       1     1.773
+	 Cl     4     C     1       1     1.7993
+	 Cl     1     C     1       2     1.72
+	 Cl     1     C     2       2     1.72
+	 Cl     1     C     3       2     1.7018
+	 Cl     1     C     4       2     1.767
+	 Cl     2     C     1       2     1.72
+	 Cl     3     C     1       2     1.72
+	 Cl     4     C     1       2     1.7425
+	 Cl     1     C     1       3     1.4231
+	 Cl     1     C     2       3     1.7739
+	 Cl     1     C     3       3     1.7018
+	 Cl     1     C     4       3     1.767
+	 Cl     2     C     1       3     1.4231
+	 Cl     3     C     1       3     1.423
+	 Cl     4     C     1       3     1.4294
+	 Cl     1     N     1       1     1.7292
+	 Cl     1     N     2       1     1.7292
+	 Cl     1     N     3       1     1.761
+	 Cl     1     N     4       1     1.725
+	 Cl     1     N     5       1     1.8244
+	 Cl     2     N     1       1     1.7291
+	 Cl     3     N     1       1     1.7292
+	 Cl     4     N     1       1     1.7485
+	 Cl     1     N     1       2     1.5292
+	 Cl     1     N     2       2     1.5292
+	 Cl     1     N     3       2     1.5292
+	 Cl     1     N     4       2     1.5515
+	 Cl     1     N     5       2     1.5638
+	 Cl     2     N     1       2     1.5292
+	 Cl     3     N     1       2     1.5292
+	 Cl     4     N     1       2     1.5376
+	 Cl     1     N     1       3     1.6492
+	 Cl     1     N     2       3     1.6956
+	 Cl     1     N     3       3     1.6492
+	 Cl     1     N     4       3     1.6884
+	 Cl     1     N     5       3     1.7114
+	 Cl     2     N     1       3     1.6492
+	 Cl     3     N     1       3     1.6492
+	 Cl     4     N     1       3     1.6631
+	 Cl     1     O     1       1     1.6843
+	 Cl     1     O     2       1     1.6843
+	 Cl     1     O     3       1     1.6843
+	 Cl     2     O     1       1     1.6843
+	 Cl     3     O     1       1     1.6843
+	 Cl     4     O     1       1     1.6998
+	 Cl     1     O     1       2     1.4843
+	 Cl     1     O     2       2     1.4843
+	 Cl     1     O     3       2     1.4843
+	 Cl     2     O     1       2     1.4843
+	 Cl     3     O     1       2     1.4844
+	 Cl     4     O     1       2     1.491
+	 Cl     1     O     1       3     1.3443
+	 Cl     1     O     2       3     1.3443
+	 Cl     1     O     3       3     1.3443
+	 Cl     2     O     1       3     1.3443
+	 Cl     3     O     1       3     1.3444
+	 Cl     4     O     1       3     1.3479
+	 Cl     1     P     1       1     2.0445
+	 Cl     1     P     2       1     2.0445
+	 Cl     1     P     3       1     2.1
+	 Cl     1     P     4       1     2.0103
+	 Cl     1     P     5       1     2.0863
+	 Cl     1     P     6       1     2.1254
+	 Cl     2     P     1       1     2.0445
+	 Cl     3     P     1       1     2.0447
+	 Cl     4     P     1       1     2.0745
+	 Cl     1     P     1       2     1.8445
+	 Cl     1     P     2       2     1.8445
+	 Cl     1     P     3       2     1.8446
+	 Cl     1     P     4       2     1.8573
+	 Cl     1     P     5       2     1.8648
+	 Cl     1     P     6       2     1.8799
+	 Cl     2     P     1       2     1.8445
+	 Cl     3     P     1       2     1.8445
+	 Cl     4     P     1       2     1.8591
+	 Cl     1     P     1       3     1.7045
+	 Cl     1     P     2       3     1.7045
+	 Cl     1     P     3       3     1.7045
+	 Cl     1     P     4       3     1.7121
+	 Cl     1     P     5       3     1.7165
+	 Cl     1     P     6       3     1.7244
+	 Cl     2     P     1       3     1.7045
+	 Cl     3     P     1       3     1.7045
+	 Cl     4     P     1       3     1.7132
+	 Cl     1     S     1       1     2.031
+	 Cl     1     S     2       1     2.031
+	 Cl     1     S     3       1     2.031
+	 Cl     1     S     4       1     1.9985
+	 Cl     1     S     5       1     1.9855
+	 Cl     1     S     6       1     1.9827
+	 Cl     2     S     1       1     2.031
+	 Cl     3     S     1       1     2.031
+	 Cl     4     S     1       1     2.0566
+	 Cl     1     S     1       2     2.031
+	 Cl     1     S     2       2     2.031
+	 Cl     1     S     3       2     2.031
+	 Cl     1     S     4       2     1.9985
+	 Cl     1     S     5       2     1.9855
+	 Cl     1     S     6       2     1.9827
+	 Cl     2     S     1       2     2.031
+	 Cl     3     S     1       2     2.031
+	 Cl     4     S     1       2     2.0566
+	 Cl     1     S     1       3     2.031
+	 Cl     1     S     2       3     2.031
+	 Cl     1     S     3       3     2.031
+	 Cl     1     S     4       3     1.9985
+	 Cl     1     S     5       3     1.9855
+	 Cl     1     S     6       3     1.9827
+	 Cl     2     S     1       3     2.031
+	 Cl     3     S     1       3     2.031
+	 Cl     4     S     1       3     2.0566
+	 Cl     1     H     1       1     1.3138
+	 Cl     2     H     1       1     1.3138
+	 Cl     3     H     1       1     1.3138
+	 Cl     4     H     1       1     1.3138
+	 Cl     1     H     1       2     1.3138
+	 Cl     2     H     1       2     1.3138
+	 Cl     3     H     1       2     1.3138
+	 Cl     4     H     1       2     1.3138
+	 Cl     1     H     1       3     1.3138
+	 Cl     2     H     1       3     1.3138
+	 Cl     3     H     1       3     1.3138
+	 Cl     4     H     1       3     1.3138
+	 Cl     1     Cl     1       1     2.02
+	 Cl     1     Cl     2       1     2.02
+	 Cl     1     Cl     3       1     2.02
+	 Cl     1     Cl     4       1     2.0439
+	 Cl     2     Cl     1       1     2.02
+	 Cl     3     Cl     1       1     2.02
+	 Cl     4     Cl     1       1     2.0439
+	 Cl     1     Cl     1       2     1.82
+	 Cl     1     Cl     2       2     1.82
+	 Cl     1     Cl     3       2     1.82
+	 Cl     1     Cl     4       2     1.8317
+	 Cl     2     Cl     1       2     1.82
+	 Cl     3     Cl     1       2     1.8201
+	 Cl     4     Cl     1       2     1.8317
+	 Cl     1     Cl     1       3     1.68
+	 Cl     1     Cl     2       3     1.68
+	 Cl     1     Cl     3       3     1.68
+	 Cl     1     Cl     4       3     1.6869
+	 Cl     2     Cl     1       3     1.68
+	 Cl     3     Cl     1       3     1.68
+	 Cl     4     Cl     1       3     1.6869
Binary file CADDSuite/data/fonts/FreeSans.ttf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/A.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,107 @@
+<node>A
+	<node>Names
+		<node>Adenine</node>
+		<node>Adenin</node>
+		<node>A</node>
+	</node>
+	<node>Atoms
+		<node>P<value>P 23.872 39.165 31.119</value></node>
+		<node>O1P<value>O 25.231 39.217 30.523</value></node>
+		<node>O2P<value>O 22.847 40.110 30.636</value></node>
+		<node>O5*<value>O 24.015 39.407 32.681</value></node>
+		<node>C5*<value>C 23.898 38.444 33.717</value></node>
+		<node>1H5*<value>H 23.427 37.536 33.341</value></node>
+		<node>2H5*<value>H 23.266 38.889 34.485</value></node>
+		<node>C4*<value>C 25.259 38.091 34.326</value></node>
+		<node>H4*<value>H 25.156 37.622 35.304</value></node>
+		<node>O4*<value>O 25.979 37.144 33.552</value></node>
+		<node>C3*<value>C 26.180 39.302 34.326</value></node>
+		<node>H3*<value>H 26.158 39.977 33.470</value></node>
+		<node>O3*<value>O 25.805 40.074 35.470</value></node>
+		<node>C2*<value>C 27.544 38.641 34.414</value></node>
+		<node>1H2*<value>H 28.301 39.314 34.011</value></node>
+		<node>2H2*<value>H 27.774 38.419 35.456</value></node>
+		<node>C1*<value>C 27.277 37.165 34.164</value></node>
+		<node>H1*<value>H 27.382 36.562 35.066</value></node>
+		<node>N9<value>N 28.236 36.536 33.230</value></node>
+		<node>C8<value>C 28.440 36.783 31.901</value></node>
+		<node>H8<value>H 27.912 37.594 31.421</value></node>
+		<node>N7<value>N 29.329 36.020 31.347</value></node>
+		<node>C5<value>C 29.751 35.206 32.384</value></node>
+		<node>C6<value>C 30.698 34.181 32.452</value></node>
+		<node>N6<value>N 31.417 33.777 31.410</value></node>
+		<node>1H6<value>H 32.088 33.030 31.518</value></node>
+		<node>2H6<value>H 31.292 34.217 30.509</value></node>
+		<node>N1<value>N 30.867 33.595 33.636</value></node>
+		<node>C2<value>C 30.158 33.991 34.674</value></node>
+		<node>2H<value>H 30.296 33.518 35.635</value></node>
+		<node>N3<value>N 29.245 34.933 34.744</value></node>
+		<node>C4<value>C 29.090 35.512 33.538</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>P O1P s</value></node>
+		<node>2<value>P O2P d</value></node>
+		<node>3<value>P O5* s</value></node>
+		<node>4<value>O5* C5* s</value></node>
+		<node>5<value>C5* C4* s</value></node>
+		<node>6<value>C4* O4* s</value></node>
+		<node>7<value>C4* C3* s</value></node>
+		<node>8<value>C3* O3* s</value></node>
+		<node>9<value>C3* C2* s</value></node>
+		<node>10<value>C2* C1* s</value></node>
+		<node>11<value>C1* O4* s</value></node>
+		<node>12<value>C1* N9 s</value></node>
+		<node>13<value>N9 C8 s</value></node>
+		<node>14<value>C8 N7 d</value></node>
+		<node>15<value>N7 C5 s</value></node>
+		<node>16<value>C5 C6 s</value></node>
+		<node>17<value>C5 C4 d</value></node>
+		<node>18<value>C4 N9 s</value></node>
+		<node>19<value>C6 N6 s</value></node>
+		<node>20<value>C6 N1 d</value></node>
+		<node>21<value>N1 C2 s</value></node>
+		<node>22<value>C2 N3 d</value></node>
+		<node>23<value>N3 C4 s</value></node>
+		<node>24<value>C5* 1H5* s</value></node>
+		<node>25<value>C5* 2H5* s</value></node>
+		<node>26<value>C4* H4* s</value></node>
+		<node>27<value>C1* H1* s</value></node>
+		<node>28<value>C3* H3* s</value></node>
+		<node>29<value>C2* 1H2* s</value></node>
+    <node>30<value>C2* 2H2* s</value></node>
+		<node>31<value>C8 H8 s</value></node>
+		<node>32<value>N6 1H6 s</value></node>
+		<node>33<value>N6 2H6 s</value></node>
+		<node>34<value>C2 2H s</value></node>
+ 	</node>
+	<node>Connections
+		<node>5-term<value>P 3-term s 1.62 0.5</value></node>
+		<node>3-term<value>O3* 5-term s 1.62 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>NUCLEOTIDE</node>
+	</node>
+	<node>Variants
+    		<node>A-M
+      			<node>Properties
+        			<node>5_PRIME</node>
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>Default
+      			<node>Properties
+      			</node>
+    		</node>
+    		<node>A-3
+      			<node>Properties
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>A-5
+      			<node>Properties
+        			<node>5_PRIME</node>
+      			</node>
+    		</node>
+ 	</node>
+</node>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ACE.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,47 @@
+<node>ACE
+	<node>Names
+		<node>ACE</node>
+		<node>acetic acid</node>
+	</node>
+	<node>Atoms
+		<node>C<value>C -0.710977 -1.12008 0.000774821</value></node>
+		<node>CH3<value>C 0.0997794 -2.40762 0.00202052</value></node>
+		<node>O<value>O -1.92224 -1.17518 0.00112378</value></node>
+		<node>1HH3<value>H -0.167239 -2.98461 0.880642</value></node>
+		<node>2HH3<value>H 1.1711 -2.24422 -0.00400307</value></node>
+		<node>3HH3<value>H -0.176322 -2.99236 -0.868617</value></node>
+		<node>OXT<value>O -0.0809243 0.0851695 -0.000720861</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>C CH3 s</value></node>
+		<node>2<value>C O d</value></node>
+		<node>3<value>C OXT s</value></node>
+		<node>4<value>CH3 1HH3 s</value></node>
+		<node>5<value>CH3 2HH3 s</value></node>
+		<node>6<value>CH3 3HH3 s</value></node>
+	</node>
+	<node>Connections
+		<node>C-term
+			<value>C N-term s 1.33 0.5
+			</value>
+		</node>
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>ACE-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+    <node>ACE-M
+      <node>Properties
+        <node>C_TERMINAL</node>
+        <node>N_TERMINAL</node>
+      </node>
+    </node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ALA.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,82 @@
+<node>ALA
+	<node>Names
+		<node>Alanine</node>
+		<node>Alanin</node>
+		<node>Ala</node>
+		<node>A</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.09952427 1.425946 -0.01392276</value></node>
+		<node>3H<value>H 0.9122966 2.021833 0.09543685</value></node>
+		<node>CA<value>C -0.6343572 1.904422 -1.199327</value></node>
+		<node>HA<value>H -0.06613517 1.608824 -2.082189</value></node>
+		<node>C<value>C -0.7061328 3.434369 -1.195026</value></node>
+		<node>O<value>O 0.2770563 4.020259 -0.6877273</value></node>
+		<node>CB<value>C -2.018631 1.250585 -1.273356</value></node>
+		<node>1HB<value>H -2.525042 1.535779 -2.196084</value></node>
+		<node>2HB<value>H -1.909473 0.1656088 -1.256012</value></node>
+		<node>3HB<value>H -2.621985 1.560564 -0.4192078</value></node>
+		<node>OXT<value>O -1.554726 3.968913 -1.942107</value></node>
+		<node>1H<value>H -0.4859746 1.514033 0.8043322</value></node>
+		<node>2H<value>H 0.3756785 0.4622824 -0.137128</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>3HB CB s</value></node>
+		<node>22<value>OXT C s</value></node>
+		<node>23<value>1H N s</value></node>
+		<node>24<value>2H N s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT<value></value></node>
+				<node>1H<value></value></node>
+				<node>2H<value></value></node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>ALA-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>ALA-C
+			<node>Delete
+				<node>1H<value></value></node>
+				<node>2H<value></value></node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>ALA-N
+			<node>Delete
+				<node>OXT<value></value></node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ARG.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,110 @@
+<node>ARG
+	<node>Names
+		<node>Arginine</node>
+		<node>Arginin</node>
+		<node>Arg</node>
+		<node>R</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.04658213 1.228698 -0.008203848</value></node>
+		<node>3H<value>H 1.029144 1.468065 -0.01885969</value></node>
+		<node>CA<value>C -0.651675 1.900984 -1.120636</value></node>
+		<node>HA<value>H -0.1560273 1.589999 -2.041618</value></node>
+		<node>C<value>C -0.5384113 3.425156 -1.007164</value></node>
+		<node>O<value>O -0.4560871 4.056512 -2.083366</value></node>
+		<node>CB<value>C -2.115081 1.438444 -1.186192</value></node>
+		<node>1HB<value>H -2.126043 0.3475202 -1.20068</value></node>
+		<node>2HB<value>H -2.643967 1.778842 -0.2945162</value></node>
+		<node>CG<value>C -2.829752 1.953359 -2.443151</value></node>
+		<node>1HG<value>H -2.889884 3.042607 -2.412891</value></node>
+		<node>2HG<value>H -2.25911 1.654155 -3.324525</value></node>
+		<node>CD<value>C -4.246704 1.376451 -2.533151</value></node>
+		<node>1HD<value>H -4.174877 0.2870844 -2.574071</value></node>
+		<node>2HD<value>H -4.797596 1.672022 -1.637285</value></node>
+		<node>NE<value>N -4.940577 1.875193 -3.731703</value></node>
+		<node>HE<value>H -4.414851 2.512341 -4.314554</value></node>
+		<node>CZ<value>C -6.193176 1.546153 -4.088384</value></node>
+		<node>NH1<value>N -6.900425 0.7030471 -3.327994</value></node>
+		<node>1HH1<value>H -6.480561 0.3232263 -2.492691</value></node>
+		<node>2HH1<value>H -7.843661 0.4323652 -3.563007</value></node>
+		<node>NH2<value>N -6.730267 2.060851 -5.200565</value></node>
+		<node>1HH2<value>H -6.201764 2.698435 -5.778988</value></node>
+		<node>2HH2<value>H -7.669785 1.826959 -5.486362</value></node>
+		<node>OXT<value>O -0.796168 3.930999 0.1074273</value></node>
+		<node>1H<value>H -0.3621705 1.521632 0.867786</value></node>
+		<node>2H<value>H -0.05222332 0.2284002 -0.1067282</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>CG CB s</value></node>
+		<node>25<value>1HG CG s</value></node>
+		<node>26<value>2HG CG s</value></node>
+		<node>27<value>CD CG s</value></node>
+		<node>31<value>1HD CD s</value></node>
+		<node>32<value>2HD CD s</value></node>
+		<node>33<value>NE CD s</value></node>
+		<node>36<value>HE NE s</value></node>
+		<node>37<value>CZ NE s</value></node>
+		<node>40<value>NH1 CZ a</value></node>
+		<node>43<value>1HH1 NH1 s</value></node>
+		<node>44<value>2HH1 NH1 s</value></node>
+		<node>45<value>NH2 CZ a</value></node>
+		<node>48<value>1HH2 NH2 s</value></node>
+		<node>49<value>2HH2 NH2 s</value></node>
+		<node>50<value>OXT C s</value></node>
+		<node>51<value>1H N s</value></node>
+		<node>52<value>2H N s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>ARG-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>ARG-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>ARG-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ASN.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,90 @@
+<node>ASN
+	<node>Names
+		<node>Asparagine</node>
+		<node>Asparagin</node>
+		<node>Asn</node>
+		<node>N</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N -0.01239826 1.297873 -0.0455736</value></node>
+		<node>3H<value>H 0.8807231 1.768826 0.03701005</value></node>
+		<node>CA<value>C -0.7474616 1.91653 -1.164926</value></node>
+		<node>HA<value>H -0.1937652 1.691628 -2.077897</value></node>
+		<node>C<value>C -0.757567 3.441771 -1.010304</value></node>
+		<node>O<value>O 0.3769885 3.962902 -0.9276295</value></node>
+		<node>CB<value>C -2.149851 1.302218 -1.30196</value></node>
+		<node>1HB<value>H -2.042859 0.2235991 -1.423685</value></node>
+		<node>2HB<value>H -2.723301 1.490943 -0.3934487</value></node>
+		<node>CG<value>C -2.91901 1.84635 -2.50453</value></node>
+		<node>OD1<value>O -2.442698 2.721974 -3.218464</value></node>
+		<node>ND2<value>N -4.125435 1.339006 -2.736042</value></node>
+		<node>1HD2<value>H -4.50376 0.6180301 -2.140929</value></node>
+		<node>2HD2<value>H -4.647904 1.686222 -3.525954</value></node>
+		<node>1H<value>H -0.5352049 1.417775 0.8102037</value></node>
+		<node>2H<value>H 0.1272759 0.3139404 -0.2256562</value></node>
+		<node>OXT<value>O -1.806735 3.963976 -0.572751</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>CG CB s</value></node>
+		<node>24<value>OD1 CG d</value></node>
+		<node>25<value>ND2 CG s</value></node>
+		<node>28<value>1HD2 ND2 s</value></node>
+		<node>29<value>2HD2 ND2 s</value></node>
+		<node>30<value>1H N s</value></node>
+		<node>31<value>2H N s</value></node>
+		<node>32<value>OXT C s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>ASN-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>ASN-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>ASN-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ASP.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,86 @@
+<node>ASP
+	<node>Names
+		<node>Aspartate</node>
+		<node>Aspartat</node>
+		<node>Asp</node>
+		<node>D</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.1006113 1.231053 -0.1065504</value></node>
+		<node>3H<value>H 0.7826706 1.919109 0.1901606</value></node>
+		<node>CA<value>C -0.6776782 1.854581 -1.196471</value></node>
+		<node>HA<value>H -0.140641 1.67647 -2.129506</value></node>
+		<node>C<value>C -0.7684437 3.377808 -1.00658</value></node>
+		<node>O<value>O -0.1755398 3.814352 0.008837678</value></node>
+		<node>CB<value>C -2.059715 1.201639 -1.304611</value></node>
+		<node>1HB<value>H -1.947421 0.1437317 -1.541582</value></node>
+		<node>2HB<value>H -2.583309 1.296861 -0.3531539</value></node>
+		<node>CG<value>C -2.895658 1.868856 -2.384729</value></node>
+		<node>OD1<value>O -2.861295 1.365629 -3.526181</value></node>
+		<node>OD2<value>O -3.508188 2.905267 -2.052321</value></node>
+		<node>OXT<value>O -0.9198192 4.048685 -2.051676</value></node>
+		<node>1H<value>H -0.5109496 1.02733 0.6709606</value></node>
+		<node>2H<value>H 0.5472904 0.3836241 -0.4264945</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>CG CB s</value></node>
+		<node>24<value>OD1 CG a</value></node>
+		<node>25<value>OD2 CG a</value></node>
+		<node>26<value>OXT C s</value></node>
+		<node>27<value>1H N s</value></node>
+		<node>28<value>2H N s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>ASP-M
+			<node>Properties
+				<node>N_TERMINAL</node>
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>ASP-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>ASP-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Benzene-Skeleton.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,23 @@
+<node>Benzene-Skeleton
+	<node>Names
+		<node>Benzene-Skeleton</node>
+	</node>
+	<node>Atoms
+		<node>C1<value>C 0.066248 -1.287634 0.144514</value></node>
+		<node>C2<value>C 0.057081 -0.613884 1.337852</value></node>
+		<node>C3<value>C 0.045766 0.796088 1.307799</value></node>
+		<node>C4<value>C 0.054862 1.462219 0.071058</value></node>
+		<node>C5<value>C 0.073086 0.728404 -1.129738</value></node>
+		<node>C6<value>C 0.091744 -0.671622 -1.107443</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>C1 C2 s</value></node>
+		<node>2<value>C2 C3 d</value></node>
+		<node>3<value>C3 C4 s</value></node>
+		<node>4<value>C4 C5 d</value></node>
+		<node>5<value>C5 C6 s</value></node>
+		<node>6<value>C6 C1 d</value></node>
+	</node>
+	<node>Properties
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/C.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,102 @@
+<node>C
+	<node>Names
+		<node>Cytosine</node>
+		<node>Cytosin</node>
+		<node>C</node>
+	</node>
+	<node>Atoms
+		<node>P<value>P 15.644 29.327 35.222</value></node>
+		<node>O1P<value>O 15.393 28.440 36.382</value></node>
+		<node>O2P<value>O 14.638 30.335 34.831</value></node>
+		<node>O5*<value>O 15.947 28.383 33.968</value></node>
+		<node>C5*<value>C 16.069 28.915 32.657</value></node>
+		<node>1H5*<value>H 16.821 29.704 32.690</value></node>
+		<node>2H5*<value>H 15.119 29.333 32.322</value></node>
+		<node>C4*<value>C 16.513 27.844 31.682</value></node>
+		<node>H4*<value>H 16.609 28.228 30.666</value></node>
+		<node>O4*<value>O 17.830 27.370 32.014</value></node>
+		<node>C3*<value>C 15.542 26.637 31.746</value></node>
+		<node>H3*<value>H 14.654 26.736 32.370</value></node>
+		<node>O3*<value>O 15.186 26.233 30.429</value></node>
+		<node>C2*<value>C 16.448 25.569 32.322</value></node>
+		<node>1H2*<value>H 16.102 25.297 33.319</value></node>
+		<node>2H2*<value>H 16.428 24.689 31.678</value></node>
+		<node>C1*<value>C 17.781 25.967 31.722</value></node>
+		<node>H1*<value>H 17.935 25.853 30.649</value></node>
+		<node>N1<value>N 18.940 25.252 32.322</value></node>
+		<node>C6<value>C 18.970 24.882 33.637</value></node>
+		<node>H6<value>H 18.141 25.127 34.285</value></node>
+		<node>C5<value>C 20.022 24.211 34.147</value></node>
+		<node>H5<value>H 20.029 23.926 35.199</value></node>
+		<node>C4<value>C 21.100 23.907 33.243</value></node>
+		<node>N4<value>N 22.167 23.241 33.694</value></node>
+		<node>1H4<value>H 22.908 23.042 33.037</value></node>
+		<node>2H4<value>H 22.216 22.954 34.661</value></node>
+		<node>N3<value>N 21.059 24.280 31.953</value></node>
+		<node>C2<value>C 19.992 24.955 31.461</value></node>
+		<node>O2<value>O 19.963 25.291 30.279</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>P O1P s</value></node>
+		<node>2<value>P O2P d</value></node>
+		<node>3<value>P O5* s</value></node>
+		<node>4<value>O5* C5* s</value></node>
+		<node>5<value>C5* C4* s</value></node>
+		<node>6<value>C4* O4* s</value></node>
+		<node>7<value>C4* C3* s</value></node>
+		<node>8<value>C3* O3* s</value></node>
+		<node>9<value>C3* C2* s</value></node>
+		<node>10<value>C2* C1* s</value></node>
+		<node>11<value>C1* O4* s</value></node>
+		<node>12<value>C1* N1 s</value></node>
+		<node>13<value>N1 C6 s</value></node>
+		<node>14<value>C6 C5 d</value></node>
+		<node>15<value>C5 C4 s</value></node>
+		<node>16<value>C4 N4 s</value></node>
+		<node>17<value>C4 N3 d</value></node>
+		<node>18<value>N3 C2 s</value></node>
+		<node>19<value>C2 O2 d</value></node>
+		<node>20<value>C2 N1 s</value></node>
+		<node>21<value>C5* 1H5* s</value></node>
+		<node>22<value>C5* 2H5* s</value></node>
+		<node>23<value>C4* H4* s</value></node>
+		<node>24<value>C1* H1* s</value></node>
+		<node>25<value>C3* H3* s</value></node>
+		<node>26<value>C2* 1H2* s</value></node>
+    <node>27<value>C2* 2H2* s</value></node>
+		<node>28<value>C6 H6 s</value></node>
+		<node>29<value>C5 H5 s</value></node>
+		<node>30<value>N4 1H4 s</value></node>
+		<node>31<value>N4 2H4 s</value></node>
+ 	</node>
+	<node>Connections
+		<node>5-term<value>P 3-term s 1.62 0.5</value></node>
+		<node>3-term<value>O3* 5-term s 1.62 0.5</value></node>
+	</node>
+	<node>Properties
+    		<node>NUCLEOTIDE</node>
+  	</node>
+  	<node>Variants
+    		<node>C-M
+      			<node>Properties
+        			<node>5_PRIME</node>
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>Default
+      			<node>Properties
+      			</node>
+    		</node>
+    		<node>C-3
+      			<node>Properties
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>C-5
+      			<node>Properties
+        			<node>5_PRIME</node>
+      			</node>
+    		</node>
+  	</node>
+</node>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/CA.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,18 @@
+<node>CA
+	<node>Names
+ 		<node>Calcium ion</node>
+ 		<node>Ca2+</node>
+	</node>
+	<node>Atoms
+		<node>CA<value>Ca 0.0 0.0 0.0</value></node>
+	</node>
+	<node>Bonds
+	</node>
+	<node>Connections
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>Default</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/CYS.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,123 @@
+<node>CYS
+	<node>Names
+		<node>Cysteine</node>
+		<node>Cystein</node>
+		<node>Cys</node>
+		<node>C</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.02405081 1.288152 -0.04523527</value></node>
+		<node>3H<value>H 0.9139157 1.764642 0.02587458</value></node>
+		<node>CA<value>C -0.7231978 1.84877 -1.18869</value></node>
+		<node>HA<value>H -0.1383485 1.663318 -2.090963</value></node>
+		<node>C<value>C -0.8891953 3.364114 -1.049031</value></node>
+		<node>O<value>O 0.1143772 4.039036 -1.368143</value></node>
+		<node>CB<value>C -2.074845 1.154028 -1.367605</value></node>
+		<node>1HB<value>H -1.930864 0.09969049 -1.603445</value></node>
+		<node>2HB<value>H -2.672614 1.244251 -0.4604313</value></node>
+		<node>SG<value>S -2.936402 1.968095 -2.733035</value></node>
+		<node>HG<value>H -4.084388 1.292503 -2.621688</value></node>
+		<node>1H<value>H -0.5030248 1.428972 0.8047693</value></node>
+		<node>2H<value>H 0.1769028 0.3003187 -0.1898637</value></node>
+		<node>OXT<value>O -1.790595 3.760744 -0.2774832</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>SG CB s</value></node>
+		<node>25<value>HG SG s</value></node>
+		<node>28<value>1H N s</value></node>
+		<node>29<value>2H N s</value></node>
+		<node>30<value>OXT C s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+		<node>S-term<value>SG S-term s 2.05 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>CYS-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>CYS-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>CYS-S
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+				<node>HG</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>HAS_SSBOND</node>
+			</node>
+		</node>
+		<node>CYS-CS
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+				<node>HG</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>HAS_SSBOND</node>
+			</node>
+		</node>
+		<node>CYS-NS
+			<node>Delete
+				<node>OXT</node>
+				<node>HG</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+				<node>HAS_SSBOND</node>
+			</node>
+		</node>
+		<node>CYS-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Editing-Fragments.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,47 @@
+<node>Fragments
+	<node>#include:ALA<value>fragments/ALA.db:/ALA</value></node>
+	<node>#include:ARG<value>fragments/ARG.db:/ARG</value></node>
+	<node>#include:ASP<value>fragments/ASP.db:/ASP</value></node>
+	<node>#include:ASN<value>fragments/ASN.db:/ASN</value></node>
+	<node>#include:CYS<value>fragments/CYS.db:/CYS</value></node>
+	<node>#include:GLN<value>fragments/GLN.db:/GLN</value></node>
+	<node>#include:GLU<value>fragments/GLU.db:/GLU</value></node>
+	<node>#include:GLY<value>fragments/GLY.db:/GLY</value></node>
+	<node>#include:HIS<value>fragments/HIS.db:/HIS</value></node>
+	<node>#include:ILE<value>fragments/ILE.db:/ILE</value></node>
+	<node>#include:LEU<value>fragments/LEU.db:/LEU</value></node>
+	<node>#include:LYS<value>fragments/LYS.db:/LYS</value></node>
+	<node>#include:MET<value>fragments/MET.db:/MET</value></node>
+	<node>#include:PHE<value>fragments/PHE.db:/PHE</value></node>
+	<node>#include:PRO<value>fragments/PRO.db:/PRO</value></node>
+	<node>#include:SER<value>fragments/SER.db:/SER</value></node>
+	<node>#include:THR<value>fragments/THR.db:/THR</value></node>
+	<node>#include:TRP<value>fragments/TRP.db:/TRP</value></node>
+	<node>#include:TYR<value>fragments/TYR.db:/TYR</value></node>
+	<node>#include:VAL<value>fragments/VAL.db:/VAL</value></node>
+	<node>#include:PCA<value>fragments/PCA.db:/PCA</value></node>
+	<node>#include:ACE<value>fragments/ACE.db:/ACE</value></node>
+	<node>#include:NME<value>fragments/NME.db:/NME</value></node>
+	<node>#include:CA<value>fragments/CA.db:/CA</value></node>
+	<node>#include:MG<value>fragments/MG.db:/MG</value></node>
+	<node>#include:ZN<value>fragments/ZN.db:/ZN</value></node>
+	<node>#include:HOH<value>fragments/HOH.db:/HOH</value></node>
+	<node>#include:A<value>fragments/A.db:/A</value></node>
+	<node>#include:C<value>fragments/C.db:/C</value></node>
+	<node>#include:G<value>fragments/G.db:/G</value></node>
+	<node>#include:T<value>fragments/T.db:/T</value></node>
+	<node>#include:U<value>fragments/U.db:/U</value></node>
+	<node>#include:Pyrrole-Skeleton<value>fragments/Pyrrole-Skeleton.db:/Pyrrole-Skeleton</value></node>
+	<node>#include:Benzene-Skeleton<value>fragments/Benzene-Skeleton.db:/Benzene-Skeleton</value></node>
+	<node>#include:Indole-Skeleton<value>fragments/Indole-Skeleton.db:/Indole-Skeleton</value></node>
+</node>
+<node>Names
+	<node>#include:Discover<value>fragments/Names.Discover.db:/Discover</value></node>
+	<node>#include:Amber<value>fragments/Names.Amber.db:/Amber</value></node>
+	<node>#include:CHARMM<value>fragments/Names.CHARMM.db:/CHARMM</value></node>
+	<node>#include:XPLOR<value>fragments/Names.XPLOR.db:/XPLOR</value></node>
+	<node>#include:Star<value>fragments/Names.Star.db:/Star</value></node>
+</node>
+<node>Defaults
+	<node>Naming<value>PDB</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Fragments.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,46 @@
+<node>Fragments
+	<node>#include:ALA<value>fragments/ALA.db:/ALA</value></node>
+	<node>#include:ARG<value>fragments/ARG.db:/ARG</value></node>
+	<node>#include:ASP<value>fragments/ASP.db:/ASP</value></node>
+	<node>#include:ASN<value>fragments/ASN.db:/ASN</value></node>
+	<node>#include:CYS<value>fragments/CYS.db:/CYS</value></node>
+	<node>#include:GLN<value>fragments/GLN.db:/GLN</value></node>
+	<node>#include:GLU<value>fragments/GLU.db:/GLU</value></node>
+	<node>#include:GLY<value>fragments/GLY.db:/GLY</value></node>
+	<node>#include:HIS<value>fragments/HIS.db:/HIS</value></node>
+	<node>#include:ILE<value>fragments/ILE.db:/ILE</value></node>
+	<node>#include:LEU<value>fragments/LEU.db:/LEU</value></node>
+	<node>#include:LYS<value>fragments/LYS.db:/LYS</value></node>
+	<node>#include:MET<value>fragments/MET.db:/MET</value></node>
+	<node>#include:MSE<value>fragments/MSE.db:/MSE</value></node>
+	<node>#include:PHE<value>fragments/PHE.db:/PHE</value></node>
+	<node>#include:PRO<value>fragments/PRO.db:/PRO</value></node>
+	<node>#include:SER<value>fragments/SER.db:/SER</value></node>
+	<node>#include:THR<value>fragments/THR.db:/THR</value></node>
+	<node>#include:TRP<value>fragments/TRP.db:/TRP</value></node>
+	<node>#include:TYR<value>fragments/TYR.db:/TYR</value></node>
+	<node>#include:VAL<value>fragments/VAL.db:/VAL</value></node>
+	<node>#include:PCA<value>fragments/PCA.db:/PCA</value></node>
+	<node>#include:ACE<value>fragments/ACE.db:/ACE</value></node>
+	<node>#include:NME<value>fragments/NME.db:/NME</value></node>
+	<node>#include:CA<value>fragments/CA.db:/CA</value></node>
+	<node>#include:MG<value>fragments/MG.db:/MG</value></node>
+	<node>#include:ZN<value>fragments/ZN.db:/ZN</value></node>
+	<node>#include:HOH<value>fragments/HOH.db:/HOH</value></node>
+	<node>#include:A<value>fragments/A.db:/A</value></node>
+	<node>#include:C<value>fragments/C.db:/C</value></node>
+	<node>#include:G<value>fragments/G.db:/G</value></node>
+	<node>#include:T<value>fragments/T.db:/T</value></node>
+	<node>#include:U<value>fragments/U.db:/U</value></node>
+</node>
+<node>Names
+	<node>#include:Discover<value>fragments/Names.Discover.db:/Discover</value></node>
+	<node>#include:Amber<value>fragments/Names.Amber.db:/Amber</value></node>
+	<node>#include:CHARMM<value>fragments/Names.CHARMM.db:/CHARMM</value></node>
+	<node>#include:XPLOR<value>fragments/Names.XPLOR.db:/XPLOR</value></node>
+	<node>#include:Star<value>fragments/Names.Star.db:/Star</value></node>
+	<node>#include:DNA<value>fragments/Names.DNA.db:/DNA</value></node>
+</node>
+<node>Defaults
+	<node>Naming<value>PDB</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/G.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,107 @@
+<node>G
+	<node>Names
+		<node>Guanine</node>
+		<node>Guanin</node>
+		<node>G</node>
+	</node>
+	<node>Atoms
+		<node>P<value>P 32.612 26.662 40.051</value></node>
+		<node>O1P<value>O 33.579 26.377 41.135</value></node>
+		<node>O2P<value>O 32.257 25.612 39.055</value></node>
+		<node>O5*<value>O 31.233 27.248 40.656</value></node>
+		<node>C5*<value>C 31.159 28.416 41.468</value></node>
+		<node>1H5*<value>H 32.062 29.003 41.301</value></node>
+		<node>2H5*<value>H 31.095 28.140 42.520</value></node>
+		<node>C4*<value>C 29.940 29.254 41.095</value></node>
+		<node>H4*<value>H 29.785 30.090 41.777</value></node>
+		<node>O4*<value>O 30.102 29.870 39.801</value></node>
+		<node>C3*<value>C 28.712 28.348 41.021</value></node>
+		<node>O3*<value>O 27.645 28.918 41.772</value></node>
+		<node>H3*<value>H 28.886 27.326 41.358</value></node>
+		<node>C2*<value>C 28.364 28.341 39.559</value></node>
+		<node>1H2*<value>H 28.348 27.314 39.193</value></node>
+		<node>2H2*<value>H 27.382 28.792 39.416</value></node>
+		<node>C1*<value>C 28.928 29.637 39.018</value></node>
+		<node>H1*<value>H 28.284 30.517 39.013</value></node>
+		<node>N9<value>N 29.311 29.477 37.601</value></node>
+		<node>C8<value>C 30.238 28.616 37.067</value></node>
+		<node>H8<value>H 30.771 27.925 37.703</value></node>
+		<node>N7<value>N 30.381 28.736 35.780</value></node>
+		<node>C5<value>C 29.485 29.746 35.436</value></node>
+		<node>C6<value>C 29.204 30.305 34.166</value></node>
+		<node>O6<value>O 29.745 30.037 33.101</value></node>
+		<node>N1<value>N 28.225 31.296 34.247</value></node>
+		<node>1H<value>H 27.948 31.750 33.400</value></node>
+		<node>C2<value>C 27.605 31.699 35.418</value></node>
+		<node>N2<value>N 26.693 32.662 35.319</value></node>
+		<node>1H2<value>H 26.407 33.145 34.479</value></node>
+		<node>2H2<value>H 26.252 32.956 36.179</value></node>
+		<node>N3<value>N 27.881 31.170 36.610</value></node>
+		<node>C4<value>C 28.823 30.204 36.543</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>P O1P s</value></node>
+		<node>2<value>P O2P d</value></node>
+		<node>3<value>P O5* s</value></node>
+		<node>4<value>O5* C5* s</value></node>
+		<node>5<value>C5* C4* s</value></node>
+		<node>6<value>C4* O4* s</value></node>
+		<node>7<value>C4* C3* s</value></node>
+		<node>8<value>C3* O3* s</value></node>
+		<node>9<value>C3* C2* s</value></node>
+		<node>10<value>C2* C1* s</value></node>
+		<node>11<value>C1* O4* s</value></node>
+		<node>12<value>C1* N9 s</value></node>
+		<node>13<value>N9 C8 s</value></node>
+		<node>14<value>C8 N7 d</value></node>
+		<node>15<value>N7 C5 s</value></node>
+		<node>16<value>C5 C4 d</value></node>
+		<node>17<value>C4 N9 s</value></node>
+		<node>18<value>C5 C6 s</value></node>
+		<node>19<value>C6 O6 d</value></node>
+		<node>20<value>C6 N1 s</value></node>
+		<node>21<value>N1 C2 s</value></node>
+		<node>22<value>C2 N2 s</value></node>
+		<node>23<value>C2 N3 d</value></node>
+		<node>24<value>N3 C4 s</value></node>
+		<node>25<value>C5* 1H5* s</value></node>
+		<node>26<value>C5* 2H5* s</value></node>
+		<node>27<value>C4* H4* s</value></node>
+		<node>28<value>C1* H1* s</value></node>
+		<node>29<value>C3* H3* s</value></node>
+		<node>30<value>C2* 1H2* s</value></node>
+	        <node>31<value>C2* 2H2* s</value></node>
+		<node>32<value>C8 H8 s</value></node>
+		<node>33<value>N1 1H s</value></node>
+		<node>34<value>N2 1H2 s</value></node>
+		<node>35<value>N2 2H2 s</value></node>
+ 	</node>
+	<node>Connections
+    		<node>5-term<value>P 3-term s 1.62 0.5</value></node>
+    		<node>3-term<value>O3* 5-term s 1.62 0.5</value></node>
+	</node>
+  	<node>Properties
+    		<node>NUCLEOTIDE</node>
+  		</node>
+  	<node>Variants
+    		<node>G-M
+      			<node>Properties
+        			<node>5_PRIME</node>
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>Default
+      			<node>Properties
+      			</node>
+    		</node>
+    		<node>G-5
+      		<node>Properties
+        		<node>5_PRIME</node>
+      		</node>
+    		<node>G-3
+      			<node>Properties
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+  	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/GLN.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,96 @@
+<node>GLN
+	<node>Names
+		<node>Glutamine</node>
+		<node>Glutamin</node>
+		<node>Gln</node>
+		<node>Q</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N -1.694353 -0.2940789 3.487573</value></node>
+		<node>3H<value>H -1.993324 -0.7771879 2.60663</value></node>
+		<node>CA<value>C -1.339968 1.106833 3.061471</value></node>
+		<node>HA<value>H -2.035373 1.840381 3.535663</value></node>
+		<node>C<value>C -1.613526 1.110178 1.459362</value></node>
+		<node>O<value>O -1.452083 2.138383 0.8146671</value></node>
+		<node>CB<value>C 0.1053884 1.466314 3.38408</value></node>
+		<node>2HB<value>H 0.4078564 1.068117 4.376333</value></node>
+		<node>1HB<value>H 0.7844938 0.9955081 2.644168</value></node>
+		<node>CG<value>C 0.2953307 2.976142 3.377398</value></node>
+		<node>2HG<value>H -0.08479181 3.405704 2.425381</value></node>
+		<node>1HG<value>H -0.3113416 3.443596 4.179154</value></node>
+		<node>CD<value>C 1.757013 3.318817 3.588054</value></node>
+		<node>OE1<value>O 2.263759 3.493683 4.689262</value></node>
+		<node>NE2<value>N 2.607646 3.349533 2.459146</value></node>
+		<node>2HE2<value>H 3.553186 3.659591 2.602335</value></node>
+		<node>1HE2<value>H 2.182977 3.3032491 1.543895</value></node>
+		<node>OXT<value>O -2.00241 -0.02523248 1.056456</value></node>
+		<node>2H<value>H -2.440811 -0.2844597 4.149324</value></node>
+		<node>1H<value>H -0.9086809 -0.7656706 3.887856</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>3H N s</value></node>
+		<node>2<value>CA N s</value></node>
+		<node>3<value>HA CA s</value></node>
+		<node>4<value>C CA s</value></node>
+		<node>5<value>O C d</value></node>
+		<node>6<value>CB CA s</value></node>
+		<node>7<value>2HB CB s</value></node>
+		<node>8<value>1HB CB s</value></node>
+		<node>9<value>CG CB s</value></node>
+		<node>10<value>2HG CG s</value></node>
+		<node>11<value>1HG CG s</value></node>
+		<node>12<value>CD CG s</value></node>
+		<node>13<value>OE1 CD d</value></node>
+		<node>14<value>NE2 CD s</value></node>
+		<node>15<value>2HE2 NE2 s</value></node>
+		<node>16<value>1HE2 NE2 s</value></node>
+		<node>17<value>OXT C s</value></node>
+		<node>18<value>2H N s</value></node>
+		<node>19<value>1H N s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>GLN-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>GLN-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>GLN-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/GLU.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,92 @@
+<node>GLU
+	<node>Names
+		<node>Glutamate</node>
+		<node>Glutamat</node>
+		<node>Glu</node>
+		<node>Q</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.09036078 1.20944 -0.09877955</value></node>
+		<node>3H<value>H 0.992178 1.663159 -0.02552702</value></node>
+		<node>CA<value>C -0.6644503 1.887128 -1.167784</value></node>
+		<node>HA<value>H -0.1401839 1.690991 -2.10393</value></node>
+		<node>C<value>C -0.6415405 3.403009 -0.9416856</value></node>
+		<node>O<value>O 0.5018099 3.910433 -0.8834405</value></node>
+		<node>CB<value>C -2.078524 1.299661 -1.288965</value></node>
+		<node>1HB<value>H -2.006071 0.2127525 -1.352877</value></node>
+		<node>2HB<value>H -2.670931 1.54428 -0.4052964</value></node>
+		<node>CG<value>C -2.807634 1.790975 -2.546677</value></node>
+		<node>1HG<value>H -2.881274 2.877187 -2.559357</value></node>
+		<node>2HG<value>H -2.268831 1.463546 -3.436255</value></node>
+		<node>CD<value>C -4.223983 1.236637 -2.597517</value></node>
+		<node>OE1<value>O -5.044554 1.733033 -1.797006</value></node>
+		<node>OE2<value>O -4.450723 0.3260741 -3.421581</value></node>
+		<node>1H<value>H -0.4043283 1.301303 0.7769806</value></node>
+		<node>2H<value>H 0.2085563 0.2320959 -0.3244812</value></node>
+		<node>OXT<value>O -1.674247 3.928742 -0.470977</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>CG CB s</value></node>
+		<node>25<value>1HG CG s</value></node>
+		<node>26<value>2HG CG s</value></node>
+		<node>27<value>CD CG s</value></node>
+		<node>30<value>OE1 CD a</value></node>
+		<node>31<value>OE2 CD a</value></node>
+		<node>32<value>1H N s</value></node>
+		<node>33<value>2H N s</value></node>
+		<node>34<value>OXT C s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>GLU-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>GLU-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>GLU-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/GLY.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,76 @@
+<node>GLY
+	<node>Names
+		<node>Glycine</node>
+		<node>Glycin</node>
+		<node>Gly</node>
+		<node>G</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.09000722 1.216287 -0.1108443</value></node>
+		<node>3H<value>H 0.8807056 1.803007 0.1270226</value></node>
+		<node>CA<value>C -0.6332095 1.869306 -1.215941</value></node>
+		<node>1HA<value>H -0.02850649 1.801736 -2.120623</value></node>
+		<node>2HA<value>H -1.579168 1.352425 -1.380715</value></node>
+		<node>C<value>C -0.8818576 3.344497 -0.910938</value></node>
+		<node>O<value>O 0.06351577 3.962237 -0.3713815</value></node>
+		<node>1H<value>H -0.5183882 1.138782 0.691625</value></node>
+		<node>2H<value>H 0.4027565 0.2984461 -0.3934918</value></node>
+		<node>OXT<value>O -1.901015 3.866009 -1.413833</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>1HA CA s</value></node>
+		<node>11<value>2HA CA s</value></node>
+		<node>12<value>C CA s</value></node>
+		<node>15<value>O C d</value></node>
+		<node>16<value>1H N s</value></node>
+		<node>17<value>2H N s</value></node>
+		<node>18<value>OXT C s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>GLY-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>GLY-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>GLY-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/HIS.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,99 @@
+<node>HIS
+	<node>Names
+		<node>Histidine</node>
+		<node>Histidin</node>
+		<node>His</node>
+		<node>H</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.2528806 1.616447 -0.2212145</value></node>
+		<node>3H<value>H 0.7991534 2.328624 0.245802</value></node>
+		<node>CA<value>C -0.9251888 2.215651 -0.8776516</value></node>
+		<node>HA<value>H -0.5465931 2.966134 -1.573552</value></node>
+		<node>C<value>C -1.833067 2.919479 0.1419996</value></node>
+		<node>O<value>O -2.654072 3.735267 -0.3389743</value></node>
+		<node>CB<value>C -1.677425 1.144471 -1.688265</value></node>
+		<node>1HB<value>H -0.9314069 0.53022 -2.195623</value></node>
+		<node>2HB<value>H -2.228334 0.4977131 -1.00345</value></node>
+		<node>CG<value>C -2.625881 1.668474 -2.74672</value></node>
+		<node>ND1<value>N -3.385668 2.821612 -2.671887</value></node>
+		<node>HD1<value>H -3.38348 3.467654 -1.88095</value></node>
+		<node>CD2<value>C -2.893428 1.068907 -3.947961</value></node>
+		<node>HD2<value>H -2.46763 0.1453506 -4.317409</value></node>
+		<node>CE1<value>C -4.09971 2.924621 -3.807559</value></node>
+		<node>HE1<value>H -4.788648 3.724259 -4.045286</value></node>
+		<node>NE2<value>N -3.815619 1.869323 -4.597533</value></node>
+		<node>HE2<value>H -4.210977 1.69118 -5.511979</value></node>
+		<node>1H<value>H -0.05550323 0.9331897 0.4557269</value></node>
+		<node>2H<value>H 0.827899 1.162407 -0.9164186</value></node>
+		<node>OXT<value>O -1.921441 2.400639 1.276749</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>CG CB s</value></node>
+		<node>24<value>ND1 CG a</value></node>
+		<node>27<value>HD1 ND1 s</value></node>
+		<node>28<value>CD2 CG a</value></node>
+		<node>31<value>HD2 CD2 s</value></node>
+		<node>32<value>CE1 ND1 a</value></node>
+		<node>35<value>HE1 CE1 s</value></node>
+		<node>36<value>NE2 CE1 a</value></node>
+		<node>37<value>NE2 CD2 a</value></node>
+		<node>39<value>HE2 NE2 s</value></node>
+		<node>40<value>1H N s</value></node>
+		<node>41<value>2H N s</value></node>
+		<node>42<value>OXT C s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>HIS-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>HIS-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>HIS-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/HOH.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,21 @@
+<node>HOH
+	<node>Names
+ 		<node>Water</node>
+	</node>
+	<node>Atoms
+		<node>O <value>O  15.118 9.944 8.582</value></node>
+		<node>1H<value>H  15.211 9.386 7.809</value></node>
+		<node>2H<value>H  14.173 9.992 8.730</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>1H O s</value></node>
+		<node>2<value>2H O s</value></node>
+	</node>
+	<node>Connections
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>Default</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ILE.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,100 @@
+<node>ILE
+	<node>Names
+		<node>Isoleucine</node>
+		<node>Isoleucin</node>
+		<node>Ile</node>
+		<node>I</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.1219419 1.159209 -0.1919851</value></node>
+		<node>3H<value>H 0.9740559 1.689959 -0.04711162</value></node>
+		<node>CA<value>C -0.7030041 1.935257 -1.138673</value></node>
+		<node>HA<value>H -0.2842833 1.745549 -2.127681</value></node>
+		<node>C<value>C -0.5392811 3.43721 -0.8683466</value></node>
+		<node>O<value>O 0.4636989 3.750649 -0.1867381</value></node>
+		<node>CB<value>C -2.165631 1.439687 -1.121375</value></node>
+		<node>HB<value>H -2.124804 0.349284 -1.14618</value></node>
+		<node>CG1<value>C -2.945574 1.890833 -2.370761</value></node>
+		<node>1HG1<value>H -3.189406 2.951118 -2.312008</value></node>
+		<node>2HG1<value>H -2.330654 1.72068 -3.255403</value></node>
+		<node>CG2<value>C -2.890608 1.852801 0.1693949</value></node>
+		<node>1HG2<value>H -3.851115 1.343782 0.2388784</value></node>
+		<node>2HG2<value>H -2.299751 1.573039 1.041283</value></node>
+		<node>3HG2<value>H -3.060911 2.929328 0.1868919</value></node>
+		<node>CD1<value>C -4.249351 1.108805 -2.558935</value></node>
+		<node>1HD1<value>H -4.709754 1.403511 -3.502415</value></node>
+		<node>2HD1<value>H -4.043807 0.03831363 -2.586494</value></node>
+		<node>3HD1<value>H -4.947758 1.324118 -1.751006</value></node>
+		<node>1H<value>H -0.3580201 1.071109 0.6916124</value></node>
+		<node>2H<value>H 0.3236403 0.2433889 -0.5670705</value></node>
+		<node>OXT<value>O -1.135264 4.21782 -1.641576</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>HB CB s</value></node>
+		<node>20<value>CG1 CB s</value></node>
+		<node>24<value>1HG1 CG1 s</value></node>
+		<node>25<value>2HG1 CG1 s</value></node>
+		<node>26<value>CG2 CB s</value></node>
+		<node>30<value>1HG2 CG2 s</value></node>
+		<node>31<value>2HG2 CG2 s</value></node>
+		<node>32<value>3HG2 CG2 s</value></node>
+		<node>33<value>CD1 CG1 s</value></node>
+		<node>37<value>1HD1 CD1 s</value></node>
+		<node>38<value>2HD1 CD1 s</value></node>
+		<node>39<value>3HD1 CD1 s</value></node>
+		<node>40<value>1H N s</value></node>
+		<node>41<value>2H N s</value></node>
+		<node>42<value>OXT C s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>ILE-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>ILE-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>ILE-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Indole-Skeleton.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,30 @@
+<node>Indole-Skeleton
+	<node>Names
+		<node>Indole-Skeleton</node>
+	</node>
+	<node>Atoms
+		<node>C1<value>C 0.098272 0.968184 -2.108448</value></node>
+		<node>N2<value>N 0.106846 2.054217 -1.259124</value></node>
+		<node>C3<value>C 0.08464 1.665738 0.063892</value></node>
+		<node>C4<value>C 0.060104 0.240281 0.014949</value></node>
+		<node>C5<value>C 0.062069 -0.174574 -1.386187</value></node>
+		<node>C6<value>C 0.084854 2.377612 1.27264</value></node>
+		<node>C7<value>C 0.060305 1.667968 2.483589</value></node>
+		<node>C8<value>C 0.039354 0.262233 2.470668</value></node>
+		<node>C9<value>C 0.039595 -0.441663 1.251419</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>C1 N2 s</value></node>
+		<node>2<value>N2 C3 s</value></node>
+		<node>3<value>C3 C4 d</value></node>
+		<node>4<value>C4 C5 s</value></node>
+		<node>5<value>C5 C1 d</value></node>
+		<node>6<value>C3 C6 s</value></node>
+		<node>7<value>C6 C7 d</value></node>
+		<node>8<value>C7 C8 s</value></node>
+		<node>9<value>C8 C9 d</value></node>
+		<node>10<value>C9 C4 s</value></node>
+	</node>
+	<node>Properties
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/LEU.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,100 @@
+<node>LEU
+	<node>Names
+		<node>Leucine</node>
+		<node>Leucin</node>
+		<node>Leu</node>
+		<node>L</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N -0.003476313 1.235853 0.02699674</value></node>
+		<node>3H<value>H 0.7720473 1.82942 0.3005252</value></node>
+		<node>CA<value>C -0.6514053 1.883178 -1.129898</value></node>
+		<node>HA<value>H -0.07017973 1.598957 -2.006831</value></node>
+		<node>C<value>C -0.5708863 3.410168 -0.9936234</value></node>
+		<node>O<value>O 0.1419036 3.827524 -0.05211589</value></node>
+		<node>CB<value>C -2.091007 1.359104 -1.274005</value></node>
+		<node>1HB<value>H -2.046227 0.2694775 -1.310338</value></node>
+		<node>2HB<value>H -2.646399 1.642544 -0.3785246</value></node>
+		<node>CG<value>C -2.872831 1.847369 -2.507179</value></node>
+		<node>HG<value>H -3.019899 2.926006 -2.455012</value></node>
+		<node>CD1<value>C -2.162796 1.498542 -3.821336</value></node>
+		<node>1HD1<value>H -2.800384 1.766798 -4.664294</value></node>
+		<node>2HD1<value>H -1.228827 2.051352 -3.913459</value></node>
+		<node>3HD1<value>H -1.954294 0.4288859 -3.861405</value></node>
+		<node>CD2<value>C -4.261661 1.198464 -2.502073</value></node>
+		<node>1HD2<value>H -4.845348 1.564912 -3.347144</value></node>
+		<node>2HD2<value>H -4.171115 0.1141629 -2.575422</value></node>
+		<node>3HD2<value>H -4.785489 1.451318 -1.579679</value></node>
+		<node>OXT<value>O -0.8228753 4.072413 -2.02374</value></node>
+		<node>1H<value>H -0.6580312 1.186075 0.7945588</value></node>
+		<node>2H<value>H 0.3136166 0.3082535 -0.2161924</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>25<value>HG CG s</value></node>
+    <node>26<value>CD1 CG s</value></node>
+    <node>30<value>1HD1 CD1 s</value></node>
+    <node>31<value>2HD1 CD1 s</value></node>
+    <node>32<value>3HD1 CD1 s</value></node>
+    <node>33<value>CD2 CG s</value></node>
+    <node>37<value>1HD2 CD2 s</value></node>
+    <node>38<value>2HD2 CD2 s</value></node>
+    <node>39<value>3HD2 CD2 s</value></node>
+    <node>40<value>OXT C s</value></node>
+    <node>41<value>1H N s</value></node>
+    <node>42<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>LEU-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>LEU-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>LEU-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/LYS.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,106 @@
+<node>LYS
+	<node>Names
+		<node>Lysine</node>
+		<node>Lysin</node>
+		<node>Lys</node>
+		<node>K</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.03796386 1.172592 -0.009692425</value></node>
+		<node>3H<value>H 1.016744 1.426445 0.004398665</value></node>
+		<node>CA<value>C -0.6562778 1.887361 -1.097957</value></node>
+		<node>HA<value>H -0.1455905 1.623495 -2.025311</value></node>
+		<node>C<value>C -0.5601511 3.406333 -0.9147748</value></node>
+		<node>O<value>O -0.5440148 4.087965 -1.963232</value></node>
+		<node>CB<value>C -2.114089 1.411355 -1.200695</value></node>
+		<node>1HB<value>H -2.113627 0.3206328 -1.233166</value></node>
+		<node>2HB<value>H -2.662723 1.730462 -0.3130743</value></node>
+		<node>CG<value>C -2.816849 1.934443 -2.461919</value></node>
+		<node>1HG<value>H -2.878444 3.023734 -2.425601</value></node>
+		<node>2HG<value>H -2.232982 1.645706 -3.338356</value></node>
+		<node>CD<value>C -4.230651 1.346997 -2.563318</value></node>
+		<node>1HD<value>H -4.153291 0.2577495 -2.598617</value></node>
+		<node>2HD<value>H -4.790445 1.632903 -1.669734</value></node>
+		<node>CE<value>C -4.93697 1.869824 -3.82334</value></node>
+		<node>1HE<value>H -4.991973 2.959915 -3.77821</value></node>
+		<node>2HE<value>H -4.353527 1.590667 -4.70365</value></node>
+		<node>NZ<value>N -6.304516 1.325968 -3.962642</value></node>
+		<node>1HZ<value>H -6.733165 1.692468 -4.802127</value></node>
+		<node>2HZ<value>H -6.276195 0.31765 -4.027733</value></node>
+		<node>3HZ<value>H -6.870414 1.591293 -3.16824</value></node>
+		<node>1H<value>H -0.3857403 1.416816 0.8740513</value></node>
+		<node>2H<value>H -0.04427324 0.17682 -0.1571643</value></node>
+		<node>OXT<value>O -0.7869474 3.85405 0.2308864</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>25<value>1HG CG s</value></node>
+    <node>26<value>2HG CG s</value></node>
+    <node>27<value>CD CG s</value></node>
+    <node>31<value>1HD CD s</value></node>
+    <node>32<value>2HD CD s</value></node>
+    <node>33<value>CE CD s</value></node>
+    <node>37<value>1HE CE s</value></node>
+    <node>38<value>2HE CE s</value></node>
+    <node>39<value>NZ CE s</value></node>
+    <node>43<value>1HZ NZ s</value></node>
+    <node>44<value>2HZ NZ s</value></node>
+    <node>45<value>3HZ NZ s</value></node>
+    <node>46<value>1H N s</value></node>
+    <node>47<value>2H N s</value></node>
+    <node>48<value>OXT C s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>LYS-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>LYS-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>LYS-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/MET.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,96 @@
+<node>MET
+	<node>Names
+		<node>Methionine</node>
+		<node>Methionin</node>
+		<node>Met</node>
+		<node>M</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.0654056 1.215812 -0.06949145</value></node>
+		<node>3H<value>H 0.9974914 1.608735 -0.04203663</value></node>
+		<node>CA<value>C -0.6988745 1.893029 -1.131979</value></node>
+		<node>HA<value>H -0.1911148 1.68141 -2.074138</value></node>
+		<node>C<value>C -0.6694928 3.410054 -0.9194202</value></node>
+		<node>O<value>O 0.4107355 3.973423 -1.201833</value></node>
+		<node>CB<value>C -2.121216 1.317703 -1.225039</value></node>
+		<node>1HB<value>H -2.050125 0.2325057 -1.312704</value></node>
+		<node>2HB<value>H -2.682049 1.549083 -0.318349</value></node>
+		<node>CG<value>C -2.887041 1.8377 -2.448318</value></node>
+		<node>1HG<value>H -2.99595 2.919347 -2.383954</value></node>
+		<node>2HG<value>H -2.322049 1.593525 -3.347709</value></node>
+		<node>SD<value>S -4.546617 1.137771 -2.634913</value></node>
+		<node>CE<value>C -5.081393 1.965263 -4.148402</value></node>
+		<node>1HE<value>H -6.08969 1.634787 -4.393987</value></node>
+		<node>2HE<value>H -5.078839 3.043304 -3.993342</value></node>
+		<node>3HE<value>H -4.404794 1.706412 -4.961773</value></node>
+		<node>OXT<value>O -1.565656 3.902471 -0.1992161</value></node>
+		<node>1H<value>H -0.3889995 1.363342 0.8203897</value></node>
+		<node>2H<value>H 0.1172404 0.226119 -0.264187</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>25<value>1HG CG s</value></node>
+    <node>26<value>2HG CG s</value></node>
+    <node>27<value>SD CG s</value></node>
+    <node>33<value>CE SD s</value></node>
+    <node>37<value>1HE CE s</value></node>
+    <node>38<value>2HE CE s</value></node>
+    <node>39<value>3HE CE s</value></node>
+    <node>40<value>OXT C s</value></node>
+    <node>41<value>1H N s</value></node>
+    <node>42<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>MET-M
+			<node>Properties
+				<node>N_TERMINAL</node>
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>MET-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>MET-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/MG.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,18 @@
+<node>MG
+	<node>Names
+ 		<node>Magnesium ion</node>
+ 		<node>Mg2+</node>
+	</node>
+	<node>Atoms
+		<node>MG<value>Mg 0.0 0.0 0.0</value></node>
+	</node>
+	<node>Bonds
+	</node>
+	<node>Connections
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>Default</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/MSE.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,95 @@
+<node>MSE
+	<node>Names
+		<node>Selenomethionine</node>
+		<node>Selenomethionin</node>
+		<node>Mse</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.0654056 1.215812 -0.06949145</value></node>
+		<node>3H<value>H 0.9974914 1.608735 -0.04203663</value></node>
+		<node>CA<value>C -0.6988745 1.893029 -1.131979</value></node>
+		<node>HA<value>H -0.1911148 1.68141 -2.074138</value></node>
+		<node>C<value>C -0.6694928 3.410054 -0.9194202</value></node>
+		<node>O<value>O 0.4107355 3.973423 -1.201833</value></node>
+		<node>CB<value>C -2.121216 1.317703 -1.225039</value></node>
+		<node>1HB<value>H -2.050125 0.2325057 -1.312704</value></node>
+		<node>2HB<value>H -2.682049 1.549083 -0.318349</value></node>
+		<node>CG<value>C -2.887041 1.8377 -2.448318</value></node>
+		<node>1HG<value>H -2.99595 2.919347 -2.383954</value></node>
+		<node>2HG<value>H -2.322049 1.593525 -3.347709</value></node>
+		<node>SE<value>Se -4.546617 1.137771 -2.634913</value></node>
+		<node>CE<value>C -5.081393 1.965263 -4.148402</value></node>
+		<node>1HE<value>H -6.08969 1.634787 -4.393987</value></node>
+		<node>2HE<value>H -5.078839 3.043304 -3.993342</value></node>
+		<node>3HE<value>H -4.404794 1.706412 -4.961773</value></node>
+		<node>OXT<value>O -1.565656 3.902471 -0.1992161</value></node>
+		<node>1H<value>H -0.3889995 1.363342 0.8203897</value></node>
+		<node>2H<value>H 0.1172404 0.226119 -0.264187</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>25<value>1HG CG s</value></node>
+    <node>26<value>2HG CG s</value></node>
+    <node>27<value>SE CG s</value></node>
+    <node>33<value>CE SE s</value></node>
+    <node>37<value>1HE CE s</value></node>
+    <node>38<value>2HE CE s</value></node>
+    <node>39<value>3HE CE s</value></node>
+    <node>40<value>OXT C s</value></node>
+    <node>41<value>1H N s</value></node>
+    <node>42<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>MET-M
+			<node>Properties
+				<node>N_TERMINAL</node>
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>MET-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>MET-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/NME.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,46 @@
+<node>NME
+	<node>Names
+		<node>Methylamine</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N  0.724  0.000 -0.079</value></node>
+		<node>CH3<value>C -0.742  0.000  0.011</value></node>
+		<node>1H<value>H 1.046  0.810  0.431</value></node>
+		<node>2H<value>H 1.046 -0.810  0.431</value></node>
+		<node>1HH3<value>H -1.139 -0.861 -0.527</value></node>
+		<node>2HH3<value>H -1.042 -0.056  1.057</value></node>
+		<node>3HH3<value>H -1.133  0.917 -0.431</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>N CH3 s</value></node>
+		<node>2<value>N 1H s</value></node>
+		<node>3<value>N 2H s</value></node>
+		<node>4<value>CH3 1HH3 s</value></node>
+		<node>5<value>CH3 2HH3 s</value></node>
+		<node>6<value>CH3 3HH3 s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>NME-C
+			<node>Delete
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>1H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>NME-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.Amber.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,486 @@
+<node>Amber<value>PDB</value>
+ <node>*:H1<value>*:1H</value></node>
+ <node>*:H2<value>*:2H</value></node>
+ <node>*:H3<value>*:3H</value></node>
+ <node>*:N<value>*:N</value></node>
+ <node>*:C<value>*:C</value></node>
+ <node>*:O<value>*:O</value></node>
+ <node>*:H<value>*:H</value></node>
+ <node>ALA:CA<value>ALA:CA</value></node>
+ <node>ALA:HA<value>ALA:HA</value></node>
+ <node>ALA:CB<value>ALA:CB</value></node>
+ <node>ALA:HB1<value>ALA:1HB</value></node>
+ <node>ALA:HB2<value>ALA:2HB</value></node>
+ <node>ALA:HB3<value>ALA:3HB</value></node>
+ <node>ARG:CA<value>ARG:CA</value></node>
+ <node>ARG:HA<value>ARG:HA</value></node>
+ <node>ARG:CB<value>ARG:CB</value></node>
+ <node>ARG:HB2<value>ARG:1HB</value></node>
+ <node>ARG:HB3<value>ARG:2HB</value></node>
+ <node>ARG:CG<value>ARG:CG</value></node>
+ <node>ARG:HG2<value>ARG:1HG</value></node>
+ <node>ARG:HG3<value>ARG:2HG</value></node>
+ <node>ARG:CD<value>ARG:CD</value></node>
+ <node>ARG:HD2<value>ARG:1HD</value></node>
+ <node>ARG:HD3<value>ARG:2HD</value></node>
+ <node>ARG:NE<value>ARG:NE</value></node>
+ <node>ARG:HE<value>ARG:HE</value></node>
+ <node>ARG:CZ<value>ARG:CZ</value></node>
+ <node>ARG:NH1<value>ARG:NH1</value></node>
+ <node>ARG:HH11<value>ARG:1HH1</value></node>
+ <node>ARG:HH12<value>ARG:2HH1</value></node>
+ <node>ARG:NH2<value>ARG:NH2</value></node>
+ <node>ARG:HH21<value>ARG:1HH2</value></node>
+ <node>ARG:HH22<value>ARG:2HH2</value></node>
+ <node>ASN:CA<value>ASN:CA</value></node>
+ <node>ASN:HA<value>ASN:HA</value></node>
+ <node>ASN:CB<value>ASN:CB</value></node>
+ <node>ASN:HB2<value>ASN:1HB</value></node>
+ <node>ASN:HB3<value>ASN:2HB</value></node>
+ <node>ASN:CG<value>ASN:CG</value></node>
+ <node>ASN:OD1<value>ASN:OD1</value></node>
+ <node>ASN:ND2<value>ASN:ND2</value></node>
+ <node>ASN:HD21<value>ASN:1HD2</value></node>
+ <node>ASN:HD22<value>ASN:2HD2</value></node>
+ <node>ASP:CA<value>ASP:CA</value></node>
+ <node>ASP:HA<value>ASP:HA</value></node>
+ <node>ASP:CB<value>ASP:CB</value></node>
+ <node>ASP:HB2<value>ASP:1HB</value></node>
+ <node>ASP:HB3<value>ASP:2HB</value></node>
+ <node>ASP:CG<value>ASP:CG</value></node>
+ <node>ASP:OD1<value>ASP:OD1</value></node>
+ <node>ASP:OD2<value>ASP:OD2</value></node>
+ <node>CYS:CA<value>CYS:CA</value></node>
+ <node>CYS:HA<value>CYS:HA</value></node>
+ <node>CYS:CB<value>CYS:CB</value></node>
+ <node>CYS:HB2<value>CYS:1HB</value></node>
+ <node>CYS:HB3<value>CYS:2HB</value></node>
+ <node>CYS:SG<value>CYS:SG</value></node>
+ <node>CYS:HG<value>CYS:HG</value></node>
+ <node>CYS:HSG<value>CYS:HG</value></node>
+ <node>GLU:CA<value>GLU:CA</value></node>
+ <node>GLU:HA<value>GLU:HA</value></node>
+ <node>GLU:CB<value>GLU:CB</value></node>
+ <node>GLU:HB2<value>GLU:1HB</value></node>
+ <node>GLU:HB3<value>GLU:2HB</value></node>
+ <node>GLU:CG<value>GLU:CG</value></node>
+ <node>GLU:HG2<value>GLU:1HG</value></node>
+ <node>GLU:HG3<value>GLU:2HG</value></node>
+ <node>GLU:CD<value>GLU:CD</value></node>
+ <node>GLU:OE1<value>GLU:OE1</value></node>
+ <node>GLU:OE2<value>GLU:OE2</value></node>
+ <node>GLN:CA<value>GLN:CA</value></node>
+ <node>GLN:HA<value>GLN:HA</value></node>
+ <node>GLN:CB<value>GLN:CB</value></node>
+ <node>GLN:HB2<value>GLN:1HB</value></node>
+ <node>GLN:HB3<value>GLN:2HB</value></node>
+ <node>GLN:CG<value>GLN:CG</value></node>
+ <node>GLN:HG2<value>GLN:1HG</value></node>
+ <node>GLN:HG3<value>GLN:2HG</value></node>
+ <node>GLN:CD<value>GLN:CD</value></node>
+ <node>GLN:OE1<value>GLN:OE1</value></node>
+ <node>GLN:NE2<value>GLN:NE2</value></node>
+ <node>GLN:HE21<value>GLN:1HE2</value></node>
+ <node>GLN:HE22<value>GLN:2HE2</value></node>
+ <node>GLY:CA<value>GLY:CA</value></node>
+ <node>GLY:HA2<value>GLY:1HA</value></node>
+ <node>GLY:HA3<value>GLY:2HA</value></node>
+ <node>HIS:CA<value>HIS:CA</value></node>
+ <node>HIS:HA<value>HIS:HA</value></node>
+ <node>HIS:CB<value>HIS:CB</value></node>
+ <node>HIS:HB2<value>HIS:1HB</value></node>
+ <node>HIS:HB3<value>HIS:2HB</value></node>
+ <node>HIS:CG<value>HIS:CG</value></node>
+ <node>HIS:ND1<value>HIS:ND1</value></node>
+ <node>HIS:HD1<value>HIS:HD1</value></node>
+ <node>HIS:CE1<value>HIS:CE1</value></node>
+ <node>HIS:HE1<value>HIS:HE1</value></node>
+ <node>HIS:NE2<value>HIS:NE2</value></node>
+ <node>HIS:HE2<value>HIS:HE2</value></node>
+ <node>HIS:CD2<value>HIS:CD2</value></node>
+ <node>HIS:HD2<value>HIS:HD2</value></node>
+ <node>ILE:CA<value>ILE:CA</value></node>
+ <node>ILE:HA<value>ILE:HA</value></node>
+ <node>ILE:CB<value>ILE:CB</value></node>
+ <node>ILE:HB<value>ILE:HB</value></node>
+ <node>ILE:CG2<value>ILE:CG2</value></node>
+ <node>ILE:HG21<value>ILE:1HG2</value></node>
+ <node>ILE:HG22<value>ILE:2HG2</value></node>
+ <node>ILE:HG23<value>ILE:3HG2</value></node>
+ <node>ILE:CG1<value>ILE:CG1</value></node>
+ <node>ILE:HG12<value>ILE:1HG1</value></node>
+ <node>ILE:HG13<value>ILE:2HG1</value></node>
+ <node>ILE:CD1<value>ILE:CD1</value></node>
+ <node>ILE:HD11<value>ILE:1HD1</value></node>
+ <node>ILE:HD12<value>ILE:2HD1</value></node>
+ <node>ILE:HD13<value>ILE:3HD1</value></node>
+ <node>LEU:CA<value>LEU:CA</value></node>
+ <node>LEU:HA<value>LEU:HA</value></node>
+ <node>LEU:CB<value>LEU:CB</value></node>
+ <node>LEU:HB2<value>LEU:1HB</value></node>
+ <node>LEU:HB3<value>LEU:2HB</value></node>
+ <node>LEU:CG<value>LEU:CG</value></node>
+ <node>LEU:HG<value>LEU:HG</value></node>
+ <node>LEU:CD1<value>LEU:CD1</value></node>
+ <node>LEU:HD11<value>LEU:1HD1</value></node>
+ <node>LEU:HD12<value>LEU:2HD1</value></node>
+ <node>LEU:HD13<value>LEU:3HD1</value></node>
+ <node>LEU:CD2<value>LEU:CD2</value></node>
+ <node>LEU:HD21<value>LEU:1HD2</value></node>
+ <node>LEU:HD22<value>LEU:2HD2</value></node>
+ <node>LEU:HD23<value>LEU:3HD2</value></node>
+ <node>LYS:CA<value>LYS:CA</value></node>
+ <node>LYS:HA<value>LYS:HA</value></node>
+ <node>LYS:CB<value>LYS:CB</value></node>
+ <node>LYS:HB2<value>LYS:1HB</value></node>
+ <node>LYS:HB3<value>LYS:2HB</value></node>
+ <node>LYS:CG<value>LYS:CG</value></node>
+ <node>LYS:HG2<value>LYS:1HG</value></node>
+ <node>LYS:HG3<value>LYS:2HG</value></node>
+ <node>LYS:CD<value>LYS:CD</value></node>
+ <node>LYS:HD2<value>LYS:1HD</value></node>
+ <node>LYS:HD3<value>LYS:2HD</value></node>
+ <node>LYS:CE<value>LYS:CE</value></node>
+ <node>LYS:HE2<value>LYS:1HE</value></node>
+ <node>LYS:HE3<value>LYS:2HE</value></node>
+ <node>LYS:NZ<value>LYS:NZ</value></node>
+ <node>LYS:HZ1<value>LYS:1HZ</value></node>
+ <node>LYS:HZ2<value>LYS:2HZ</value></node>
+ <node>LYS:HZ3<value>LYS:3HZ</value></node>
+ <node>MET:CA<value>MET:CA</value></node>
+ <node>MET:HA<value>MET:HA</value></node>
+ <node>MET:CB<value>MET:CB</value></node>
+ <node>MET:HB2<value>MET:1HB</value></node>
+ <node>MET:HB3<value>MET:2HB</value></node>
+ <node>MET:CG<value>MET:CG</value></node>
+ <node>MET:HG2<value>MET:1HG</value></node>
+ <node>MET:HG3<value>MET:2HG</value></node>
+ <node>MET:SD<value>MET:SD</value></node>
+ <node>MET:CE<value>MET:CE</value></node>
+ <node>MET:HE1<value>MET:1HE</value></node>
+ <node>MET:HE2<value>MET:2HE</value></node>
+ <node>MET:HE3<value>MET:3HE</value></node>
+ <node>PHE:CA<value>PHE:CA</value></node>
+ <node>PHE:HA<value>PHE:HA</value></node>
+ <node>PHE:CB<value>PHE:CB</value></node>
+ <node>PHE:HB2<value>PHE:1HB</value></node>
+ <node>PHE:HB3<value>PHE:2HB</value></node>
+ <node>PHE:CG<value>PHE:CG</value></node>
+ <node>PHE:CD1<value>PHE:CD1</value></node>
+ <node>PHE:HD1<value>PHE:HD1</value></node>
+ <node>PHE:CE1<value>PHE:CE1</value></node>
+ <node>PHE:HE1<value>PHE:HE1</value></node>
+ <node>PHE:CZ<value>PHE:CZ</value></node>
+ <node>PHE:HZ<value>PHE:HZ</value></node>
+ <node>PHE:CE2<value>PHE:CE2</value></node>
+ <node>PHE:HE2<value>PHE:HE2</value></node>
+ <node>PHE:CD2<value>PHE:CD2</value></node>
+ <node>PHE:HD2<value>PHE:HD2</value></node>
+ <node>PRO:CA<value>PRO:CA</value></node>
+ <node>PRO:HA<value>PRO:HA</value></node>
+ <node>PRO:CD<value>PRO:CD</value></node>
+ <node>PRO:HD2<value>PRO:1HD</value></node>
+ <node>PRO:HD3<value>PRO:2HD</value></node>
+ <node>PRO:CG<value>PRO:CG</value></node>
+ <node>PRO:HG2<value>PRO:1HG</value></node>
+ <node>PRO:HG3<value>PRO:2HG</value></node>
+ <node>PRO:CB<value>PRO:CB</value></node>
+ <node>PRO:HB2<value>PRO:1HB</value></node>
+ <node>PRO:HB3<value>PRO:2HB</value></node>
+ <node>SER:CA<value>SER:CA</value></node>
+ <node>SER:HA<value>SER:HA</value></node>
+ <node>SER:CB<value>SER:CB</value></node>
+ <node>SER:HB2<value>SER:1HB</value></node>
+ <node>SER:HB3<value>SER:2HB</value></node>
+ <node>SER:OG<value>SER:OG</value></node>
+ <node>SER:HG<value>SER:HG</value></node>
+ <node>THR:CA<value>THR:CA</value></node>
+ <node>THR:HA<value>THR:HA</value></node>
+ <node>THR:CB<value>THR:CB</value></node>
+ <node>THR:HB<value>THR:HB</value></node>
+ <node>THR:CG2<value>THR:CG2</value></node>
+ <node>THR:HG21<value>THR:1HG2</value></node>
+ <node>THR:HG22<value>THR:2HG2</value></node>
+ <node>THR:HG23<value>THR:3HG2</value></node>
+ <node>THR:OG1<value>THR:OG1</value></node>
+ <node>THR:HG1<value>THR:HG1</value></node>
+ <node>TRP:CA<value>TRP:CA</value></node>
+ <node>TRP:HA<value>TRP:HA</value></node>
+ <node>TRP:CB<value>TRP:CB</value></node>
+ <node>TRP:HB2<value>TRP:1HB</value></node>
+ <node>TRP:HB3<value>TRP:2HB</value></node>
+ <node>TRP:CG<value>TRP:CG</value></node>
+ <node>TRP:CD1<value>TRP:CD1</value></node>
+ <node>TRP:HD1<value>TRP:HD1</value></node>
+ <node>TRP:NE1<value>TRP:NE1</value></node>
+ <node>TRP:HE1<value>TRP:HE1</value></node>
+ <node>TRP:CE2<value>TRP:CE2</value></node>
+ <node>TRP:CZ2<value>TRP:CZ2</value></node>
+ <node>TRP:HZ2<value>TRP:HZ2</value></node>
+ <node>TRP:CH2<value>TRP:CH2</value></node>
+ <node>TRP:HH2<value>TRP:HH2</value></node>
+ <node>TRP:CZ3<value>TRP:CZ3</value></node>
+ <node>TRP:HZ3<value>TRP:HZ3</value></node>
+ <node>TRP:CE3<value>TRP:CE3</value></node>
+ <node>TRP:HE3<value>TRP:HE3</value></node>
+ <node>TRP:CD2<value>TRP:CD2</value></node>
+ <node>TYR:CA<value>TYR:CA</value></node>
+ <node>TYR:HA<value>TYR:HA</value></node>
+ <node>TYR:CB<value>TYR:CB</value></node>
+ <node>TYR:HB2<value>TYR:1HB</value></node>
+ <node>TYR:HB3<value>TYR:2HB</value></node>
+ <node>TYR:CG<value>TYR:CG</value></node>
+ <node>TYR:CD1<value>TYR:CD1</value></node>
+ <node>TYR:HD1<value>TYR:HD1</value></node>
+ <node>TYR:CE1<value>TYR:CE1</value></node>
+ <node>TYR:HE1<value>TYR:HE1</value></node>
+ <node>TYR:CZ<value>TYR:CZ</value></node>
+ <node>TYR:OH<value>TYR:OH</value></node>
+ <node>TYR:HH<value>TYR:HH</value></node>
+ <node>TYR:CE2<value>TYR:CE2</value></node>
+ <node>TYR:HE2<value>TYR:HE2</value></node>
+ <node>TYR:CD2<value>TYR:CD2</value></node>
+ <node>TYR:HD2<value>TYR:HD2</value></node>
+ <node>VAL:CA<value>VAL:CA</value></node>
+ <node>VAL:HA<value>VAL:HA</value></node>
+ <node>VAL:CB<value>VAL:CB</value></node>
+ <node>VAL:HB<value>VAL:HB</value></node>
+ <node>VAL:CG1<value>VAL:CG1</value></node>
+ <node>VAL:HG11<value>VAL:1HG1</value></node>
+ <node>VAL:HG12<value>VAL:2HG1</value></node>
+ <node>VAL:HG13<value>VAL:3HG1</value></node>
+ <node>VAL:CG2<value>VAL:CG2</value></node>
+ <node>VAL:HG21<value>VAL:1HG2</value></node>
+ <node>VAL:HG22<value>VAL:2HG2</value></node>
+ <node>VAL:HG23<value>VAL:3HG2</value></node>
+ <node>DC:P<value>C:P</value></node>
+ <node>DC:O1P<value>C:O1P</value></node>
+ <node>DC:O2P<value>C:O2P</value></node>
+ <node>DC:O5'<value>C:O5*</value></node>
+ <node>DC:C5'<value>C:C5*</value></node>
+ <node>DC:H5'1<value>C:1H5*</value></node>
+ <node>DC:H5'2<value>C:2H5*</value></node>
+ <node>DC:C4'<value>C:C4*</value></node>
+ <node>DC:H4'<value>C:H4*</value></node>
+ <node>DC:O4'<value>C:O4*</value></node>
+ <node>DC:C1'<value>C:C1*</value></node>
+ <node>DC:H1'<value>C:H1*</value></node>
+ <node>DC:N1<value>C:N1</value></node>
+ <node>DC:C6<value>C:C6</value></node>
+ <node>DC:H6<value>C:H6</value></node>
+ <node>DC:C5<value>C:C5</value></node>
+ <node>DC:H5<value>C:H5</value></node>
+ <node>DC:C4<value>C:C4</value></node>
+ <node>DC:N4<value>C:N4</value></node>
+ <node>DC:H41<value>C:1H4</value></node>
+ <node>DC:H42<value>C:2H4</value></node>
+ <node>DC:N3<value>C:N3</value></node>
+ <node>DC:C2<value>C:C2</value></node>
+ <node>DC:O2<value>C:O2</value></node>
+ <node>DC:C3'<value>C:C3*</value></node>
+ <node>DC:H3'<value>C:H3*</value></node>
+ <node>DC:C2'<value>C:C2*</value></node>
+ <node>DC:H2'1<value>C:1H2*</value></node>
+ <node>DC:H2'2<value>C:2H2*</value></node>
+ <node>DC:O3'<value>C:O3*</value></node>
+ <node>DA:P<value>A:P</value></node>
+ <node>DA:O1P<value>A:O1P</value></node>
+ <node>DA:O2P<value>A:O2P</value></node>
+ <node>DA:O5'<value>A:O5*</value></node>
+ <node>DA:C5'<value>A:C5*</value></node>
+ <node>DA:H5'1<value>A:1H5*</value></node>
+ <node>DA:H5'2<value>A:2H5*</value></node>
+ <node>DA:C4'<value>A:C4*</value></node>
+ <node>DA:H4'<value>A:H4*</value></node>
+ <node>DA:O4'<value>A:O4*</value></node>
+ <node>DA:C1'<value>A:C1*</value></node>
+ <node>DA:H1'<value>A:H1*</value></node>
+ <node>DA:N9<value>A:N9</value></node>
+ <node>DA:C8<value>A:C8</value></node>
+ <node>DA:H8<value>A:H8</value></node>
+ <node>DA:N7<value>A:N7</value></node>
+ <node>DA:C5<value>A:C5</value></node>
+ <node>DA:C6<value>A:C6</value></node>
+ <node>DA:N6<value>A:N6</value></node>
+ <node>DA:H61<value>A:1H6</value></node>
+ <node>DA:H62<value>A:2H6</value></node>
+ <node>DA:N1<value>A:N1</value></node>
+ <node>DA:C2<value>A:C2</value></node>
+ <node>DA:H2<value>A:2H</value></node>
+ <node>DA:N3<value>A:N3</value></node>
+ <node>DA:C4<value>A:C4</value></node>
+ <node>DA:C3'<value>A:C3*</value></node>
+ <node>DA:H3'<value>A:H3*</value></node>
+ <node>DA:C2'<value>A:C2*</value></node>
+ <node>DA:H2'1<value>A:1H2*</value></node>
+ <node>DA:H2'2<value>A:2H2*</value></node>
+ <node>DA:O3'<value>A:O3*</value></node>
+ <node>DT:P<value>T:P</value></node>
+ <node>DT:O1P<value>T:O1P</value></node>
+ <node>DT:O2P<value>T:O2P</value></node>
+ <node>DT:O5'<value>T:O5*</value></node>
+ <node>DT:C5'<value>T:C5*</value></node>
+ <node>DT:H5'1<value>T:1H5*</value></node>
+ <node>DT:H5'2<value>T:2H5*</value></node>
+ <node>DT:C4'<value>T:C4*</value></node>
+ <node>DT:H4'<value>T:H4*</value></node>
+ <node>DT:O4'<value>T:O4*</value></node>
+ <node>DT:C1'<value>T:C1*</value></node>
+ <node>DT:H1'<value>T:H1*</value></node>
+ <node>DT:N1<value>T:N1</value></node>
+ <node>DT:C6<value>T:C6</value></node>
+ <node>DT:H6<value>T:H6</value></node>
+ <node>DT:C5<value>T:C5</value></node>
+ <node>DT:C7<value>T:C5M</value></node>
+ <node>DT:H71<value>T:1H5M</value></node>
+ <node>DT:H72<value>T:2H5M</value></node>
+ <node>DT:H73<value>T:3H5M</value></node>
+ <node>DT:C4<value>T:C4</value></node>
+ <node>DT:O4<value>T:O4</value></node>
+ <node>DT:N3<value>T:N3</value></node>
+ <node>DT:H3<value>T:3H</value></node>
+ <node>DT:C2<value>T:C2</value></node>
+ <node>DT:O2<value>T:O2</value></node>
+ <node>DT:C3'<value>T:C3*</value></node>
+ <node>DT:H3'<value>T:H3*</value></node>
+ <node>DT:C2'<value>T:C2*</value></node>
+ <node>DT:H2'1<value>T:1H2*</value></node>
+ <node>DT:H2'2<value>T:2H2*</value></node>
+ <node>DT:O3'<value>T:O3*</value></node>
+ <node>DG:P<value>G:P</value></node>
+ <node>DG:O1P<value>G:O1P</value></node>
+ <node>DG:O2P<value>G:O2P</value></node>
+ <node>DG:O5'<value>G:O5*</value></node>
+ <node>DG:C5'<value>G:C5*</value></node>
+ <node>DG:H5'1<value>G:1H5*</value></node>
+ <node>DG:H5'2<value>G:2H5*</value></node>
+ <node>DG:C4'<value>G:C4*</value></node>
+ <node>DG:H4'<value>G:H4*</value></node>
+ <node>DG:O4'<value>G:O4*</value></node>
+ <node>DG:C1'<value>G:C1*</value></node>
+ <node>DG:H1'<value>G:H1*</value></node>
+ <node>DG:N9<value>G:N9</value></node>
+ <node>DG:C8<value>G:C8</value></node>
+ <node>DG:H8<value>G:H8</value></node>
+ <node>DG:N7<value>G:N7</value></node>
+ <node>DG:C5<value>G:C5</value></node>
+ <node>DG:C6<value>G:C6</value></node>
+ <node>DG:O6<value>G:O6</value></node>
+ <node>DG:N1<value>G:N1</value></node>
+ <node>DG:H1<value>G:1H</value></node>
+ <node>DG:C2<value>G:C2</value></node>
+ <node>DG:N2<value>G:N2</value></node>
+ <node>DG:H21<value>G:1H2</value></node>
+ <node>DG:H22<value>G:2H2</value></node>
+ <node>DG:N3<value>G:N3</value></node>
+ <node>DG:C4<value>G:C4</value></node>
+ <node>DG:C3'<value>G:C3*</value></node>
+ <node>DG:H3'<value>G:H3*</value></node>
+ <node>DG:C2'<value>G:C2*</value></node>
+ <node>DG:H2'1<value>G:1H2*</value></node>
+ <node>DG:H2'2<value>G:2H2*</value></node>
+ <node>DG:O3'<value>G:O3*</value></node>
+
+ <node>*:OXT<value>*:OXT</value></node>
+
+ <node>GLH:CA<value>GLH:CA</value></node>
+ <node>GLH:HA<value>GLH:HA</value></node>
+ <node>GLH:CB<value>GLH:CB</value></node>
+ <node>GLH:HB2<value>GLH:1HB</value></node>
+ <node>GLH:HB3<value>GLH:2HB</value></node>
+ <node>GLH:CG<value>GLH:CG</value></node>
+ <node>GLH:HG2<value>GLH:1HG</value></node>
+ <node>GLH:HG3<value>GLH:2HG</value></node>
+ <node>GLH:CD<value>GLH:CD</value></node>
+ <node>GLH:OE1<value>GLH:OE1</value></node>
+ <node>GLH:OE2<value>GLH:OE2</value></node>
+ <node>GLH:HE2<value>GLH:2HE</value></node>
+
+ <node>HID:CA<value>HID:CA</value></node>
+ <node>HID:HA<value>HID:HA</value></node>
+ <node>HID:CB<value>HID:CB</value></node>
+ <node>HID:HB2<value>HID:1HB</value></node>
+ <node>HID:HB3<value>HID:2HB</value></node>
+ <node>HID:CG<value>HID:CG</value></node>
+ <node>HID:ND1<value>HID:ND1</value></node>
+ <node>HID:HD1<value>HID:HD1</value></node>
+ <node>HID:CE1<value>HID:CE1</value></node>
+ <node>HID:HE1<value>HID:HE1</value></node>
+ <node>HID:NE2<value>HID:NE2</value></node>
+ <node>HID:HE2<value>HID:HE2</value></node>
+ <node>HID:CD2<value>HID:CD2</value></node>
+ <node>HID:HD2<value>HID:HD2</value></node>
+
+ <node>HIE:CA<value>HIE:CA</value></node>
+ <node>HIE:HA<value>HIE:HA</value></node>
+ <node>HIE:CB<value>HIE:CB</value></node>
+ <node>HIE:HB2<value>HIE:1HB</value></node>
+ <node>HIE:HB3<value>HIE:2HB</value></node>
+ <node>HIE:CG<value>HIE:CG</value></node>
+ <node>HIE:ND1<value>HIE:ND1</value></node>
+ <node>HIE:HD1<value>HIE:HD1</value></node>
+ <node>HIE:CE1<value>HIE:CE1</value></node>
+ <node>HIE:HE1<value>HIE:HE1</value></node>
+ <node>HIE:NE2<value>HIE:NE2</value></node>
+ <node>HIE:HE2<value>HIE:HE2</value></node>
+ <node>HIE:CD2<value>HIE:CD2</value></node>
+ <node>HIE:HD2<value>HIE:HD2</value></node>
+
+ <node>HIP:CA<value>HIP:CA</value></node>
+ <node>HIP:HA<value>HIP:HA</value></node>
+ <node>HIP:CB<value>HIP:CB</value></node>
+ <node>HIP:HB2<value>HIP:1HB</value></node>
+ <node>HIP:HB3<value>HIP:2HB</value></node>
+ <node>HIP:CG<value>HIP:CG</value></node>
+ <node>HIP:ND1<value>HIP:ND1</value></node>
+ <node>HIP:HD1<value>HIP:HD1</value></node>
+ <node>HIP:CE1<value>HIP:CE1</value></node>
+ <node>HIP:HE1<value>HIP:HE1</value></node>
+ <node>HIP:NE2<value>HIP:NE2</value></node>
+ <node>HIP:HE2<value>HIP:HE2</value></node>
+ <node>HIP:CD2<value>HIP:CD2</value></node>
+ <node>HIP:HD2<value>HIP:HD2</value></node>
+
+ <node>CYM:CA<value>CYM:CA</value></node>
+ <node>CYM:CB<value>CYM:CB</value></node>
+ <node>CYM:HA<value>CYM:HA</value></node>
+ <node>CYM:HB2<value>CYM:1HB</value></node>
+ <node>CYM:HB3<value>CYM:2HB</value></node>
+ <node>CYM:SG<value>CYM:SG</value></node>
+ <node>CYM:HN<value>CYM:HN</value></node>
+
+ <node>CYX:CA<value>CYX:CA</value></node>
+ <node>CYX:CB<value>CYX:CB</value></node>
+ <node>CYX:HA<value>CYX:HA</value></node>
+ <node>CYX:HB2<value>CYX:1HB</value></node>
+ <node>CYX:HB3<value>CYX:2HB</value></node>
+ <node>CYX:SG<value>CYX:SG</value></node>
+
+ <node>ACE:CH3<value>ACE:CH3</value></node>
+ <node>ACE:HH31<value>ACE:1HH3</value></node>
+ <node>ACE:HH32<value>ACE:2HH3</value></node>
+ <node>ACE:HH33<value>ACE:3HH3</value></node>
+ <node>NME:CH3<value>NME:CH3</value></node>
+ <node>NME:HH31<value>NME:1HH3</value></node>
+ <node>NME:HH32<value>NME:2HH3</value></node>
+ <node>NME:HH33<value>NME:3HH3</value></node>
+
+ <node>LYN:NZ<value>LYN:NZ</value></node>
+ <node>LYN:CA<value>LYN:CA</value></node>
+ <node>LYN:CB<value>LYN:CB</value></node>
+ <node>LYN:CG<value>LYN:CG</value></node>
+ <node>LYN:CD<value>LYN:CD</value></node>
+ <node>LYN:CE<value>LYN:CE</value></node>
+ <node>LYN:HA<value>LYN:HA</value></node>
+ <node>LYN:HB2<value>LYN:1HB</value></node>
+ <node>LYN:HB3<value>LYN:2HB</value></node>
+ <node>LYN:HD2<value>LYN:1HD</value></node>
+ <node>LYN:HD3<value>LYN:2HD</value></node>
+ <node>LYN:HE2<value>LYN:1HE</value></node>
+ <node>LYN:HE3<value>LYN:2HE</value></node>
+ <node>LYN:HG2<value>LYN:1HG</value></node>
+ <node>LYN:HG3<value>LYN:2HG</value></node>
+ <node>LYN:HZ2<value>LYN:2HZ</value></node>
+ <node>LYN:HZ3<value>LYN:3HZ</value></node>
+</node>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.CHARMM.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,279 @@
+<node>CHARMM<value>PDB</value>
+ <node>*:H1<value>*:1H</value></node>
+ <node>*:H2<value>*:2H</value></node>
+ <node>*:H3<value>*:3H</value></node>
+ <node>*:N<value>*:N</value></node>
+ <node>*:C<value>*:C</value></node>
+ <node>*:CA<value>*:CA</value></node>
+ <node>*:O<value>*:O</value></node>
+ <node>*:H<value>*:H</value></node>
+ <node>*:OT1<value>*:O</value></node>
+ <node>*:OT2<value>*:OXT</value></node>
+ <node>*:OCT1<value>*:O</value></node>
+ <node>*:OCT2<value>*:OXT</value></node>
+ <node>*:HT1<value>*:1H</value></node>
+ <node>*:HT2<value>*:2H</value></node>
+ <node>*:HT3<value>*:3H</value></node>
+ <node>ALA:HB1<value>ALA:1HB</value></node>
+ <node>ALA:HB2<value>ALA:2HB</value></node>
+ <node>ALA:HB3<value>ALA:3HB</value></node>
+ <node>ARG:HB2<value>ARG:1HB</value></node>
+ <node>ARG:HB3<value>ARG:2HB</value></node>
+ <node>ARG:HG2<value>ARG:1HG</value></node>
+ <node>ARG:HG3<value>ARG:2HG</value></node>
+ <node>ARG:HD2<value>ARG:1HD</value></node>
+ <node>ARG:HD3<value>ARG:2HD</value></node>
+ <node>ARG:HH1<value>ARG:1HH1</value></node>
+ <node>ARG:HH2<value>ARG:1HH2</value></node>
+ <node>ARG:HH11<value>ARG:1HH1</value></node>
+ <node>ARG:HH12<value>ARG:2HH1</value></node>
+ <node>ARG:HH21<value>ARG:1HH2</value></node>
+ <node>ARG:HH22<value>ARG:2HH2</value></node>
+ <node>ASN:HB2<value>ASN:1HB</value></node>
+ <node>ASN:HB3<value>ASN:2HB</value></node>
+ <node>ASN:HD1<value>ASN:1HD1</value></node>
+ <node>ASN:HD2<value>ASN:1HD2</value></node>
+ <node>ASN:HD21<value>ASN:1HD2</value></node>
+ <node>ASN:HD22<value>ASN:2HD2</value></node>
+ <node>ASP:HB2<value>ASP:1HB</value></node>
+ <node>ASP:HB3<value>ASP:2HB</value></node>
+ <node>CYS:HB2<value>CYS:1HB</value></node>
+ <node>CYS:HB3<value>CYS:2HB</value></node>
+ <node>GLU:HB2<value>GLU:1HB</value></node>
+ <node>GLU:HB3<value>GLU:2HB</value></node>
+ <node>GLU:HG2<value>GLU:1HG</value></node>
+ <node>GLU:HG3<value>GLU:2HG</value></node>
+ <node>GLN:HB2<value>GLN:1HB</value></node>
+ <node>GLN:HB3<value>GLN:2HB</value></node>
+ <node>GLN:HG2<value>GLN:1HG</value></node>
+ <node>GLN:HG3<value>GLN:2HG</value></node>
+ <node>GLN:HE21<value>GLN:1HE2</value></node>
+ <node>GLN:HE22<value>GLN:2HE2</value></node>
+ <node>GLN:HE1<value>GLN:1HE1</value></node>
+ <node>GLN:HE2<value>GLN:1HE2</value></node>
+ <node>GLY:HA2<value>GLY:1HA</value></node>
+ <node>GLY:HA3<value>GLY:2HA</value></node>
+ <node>HIS:HB2<value>HIS:1HB</value></node>
+ <node>HIS:HB3<value>HIS:2HB</value></node>
+ <node>HIE:*<value>HIS:*</value></node>
+ <node>HID:*<value>HIS:*</value></node>
+ <node>HIP:*<value>HIS:*</value></node>
+ <node>ILE:HG21<value>ILE:1HG2</value></node>
+ <node>ILE:HG22<value>ILE:2HG2</value></node>
+ <node>ILE:HG23<value>ILE:3HG2</value></node>
+ <node>ILE:HG12<value>ILE:1HG1</value></node>
+ <node>ILE:HG13<value>ILE:2HG1</value></node>
+ <node>ILE:HD11<value>ILE:1HD1</value></node>
+ <node>ILE:HD12<value>ILE:2HD1</value></node>
+ <node>ILE:HD13<value>ILE:3HD1</value></node>
+ <node>ILE:CD<value>ILE:CD1</value></node>
+ <node>LEU:HB2<value>LEU:1HB</value></node>
+ <node>LEU:HB3<value>LEU:2HB</value></node>
+ <node>LEU:HD11<value>LEU:1HD1</value></node>
+ <node>LEU:HD12<value>LEU:2HD1</value></node>
+ <node>LEU:HD13<value>LEU:3HD1</value></node>
+ <node>LEU:HD21<value>LEU:1HD2</value></node>
+ <node>LEU:HD22<value>LEU:2HD2</value></node>
+ <node>LEU:HD23<value>LEU:3HD2</value></node>
+ <node>LYS:HB2<value>LYS:1HB</value></node>
+ <node>LYS:HB3<value>LYS:2HB</value></node>
+ <node>LYS:HG2<value>LYS:1HG</value></node>
+ <node>LYS:HG3<value>LYS:2HG</value></node>
+ <node>LYS:HD2<value>LYS:1HD</value></node>
+ <node>LYS:HD3<value>LYS:2HD</value></node>
+ <node>LYS:HE2<value>LYS:1HE</value></node>
+ <node>LYS:HE3<value>LYS:2HE</value></node>
+ <node>LYS:HZ1<value>LYS:1HZ</value></node>
+ <node>LYS:HZ2<value>LYS:2HZ</value></node>
+ <node>LYS:HZ3<value>LYS:3HZ</value></node>
+ <node>MET:HB2<value>MET:1HB</value></node>
+ <node>MET:HB3<value>MET:2HB</value></node>
+ <node>MET:HG2<value>MET:1HG</value></node>
+ <node>MET:HG3<value>MET:2HG</value></node>
+ <node>MET:HE1<value>MET:1HE</value></node>
+ <node>MET:HE2<value>MET:2HE</value></node>
+ <node>MET:HE3<value>MET:3HE</value></node>
+ <node>PHE:HB2<value>PHE:1HB</value></node>
+ <node>PHE:HB3<value>PHE:2HB</value></node>
+ <node>PRO:HD2<value>PRO:1HD</value></node>
+ <node>PRO:HD3<value>PRO:2HD</value></node>
+ <node>PRO:HG2<value>PRO:1HG</value></node>
+ <node>PRO:HG3<value>PRO:2HG</value></node>
+ <node>PRO:HB2<value>PRO:1HB</value></node>
+ <node>PRO:HB3<value>PRO:2HB</value></node>
+ <node>SER:HB2<value>SER:1HB</value></node>
+ <node>SER:HB3<value>SER:2HB</value></node>
+ <node>THR:HG21<value>THR:1HG2</value></node>
+ <node>THR:HG22<value>THR:2HG2</value></node>
+ <node>THR:HG23<value>THR:3HG2</value></node>
+ <node>TRP:HB2<value>TRP:1HB</value></node>
+ <node>TRP:HB3<value>TRP:2HB</value></node>
+ <node>TYR:HB2<value>TYR:1HB</value></node>
+ <node>TYR:HB3<value>TYR:2HB</value></node>
+ <node>VAL:HG11<value>VAL:1HG1</value></node>
+ <node>VAL:HG12<value>VAL:2HG1</value></node>
+ <node>VAL:HG13<value>VAL:3HG1</value></node>
+ <node>VAL:HG21<value>VAL:1HG2</value></node>
+ <node>VAL:HG22<value>VAL:2HG2</value></node>
+ <node>VAL:HG23<value>VAL:3HG2</value></node>
+ <node>ACE:HH31<value>ACE:1HH3</value></node>
+ <node>ACE:HH32<value>ACE:2HH3</value></node>
+ <node>ACE:HH33<value>ACE:3HH3</value></node>
+ <node>NME:HH31<value>NME:1HH3</value></node>
+ <node>NME:HH32<value>NME:2HH3</value></node>
+ <node>NME:HH33<value>NME:3HH3</value></node>
+ <node>ALA:CA<value>ALA:CA</value></node>
+ <node>ALA:HA<value>ALA:HA</value></node>
+ <node>ALA:CB<value>ALA:CB</value></node>
+ <node>ARG:CA<value>ARG:CA</value></node>
+ <node>ARG:HA<value>ARG:HA</value></node>
+ <node>ARG:CB<value>ARG:CB</value></node>
+ <node>ARG:CG<value>ARG:CG</value></node>
+ <node>ARG:CD<value>ARG:CD</value></node>
+ <node>ARG:NE<value>ARG:NE</value></node>
+ <node>ARG:HE<value>ARG:HE</value></node>
+ <node>ARG:CZ<value>ARG:CZ</value></node>
+ <node>ARG:NH1<value>ARG:NH1</value></node>
+ <node>ARG:NH2<value>ARG:NH2</value></node>
+ <node>ASN:CA<value>ASN:CA</value></node>
+ <node>ASN:HA<value>ASN:HA</value></node>
+ <node>ASN:CB<value>ASN:CB</value></node>
+ <node>ASN:CG<value>ASN:CG</value></node>
+ <node>ASN:OD1<value>ASN:OD1</value></node>
+ <node>ASN:ND2<value>ASN:ND2</value></node>
+ <node>ASP:CA<value>ASP:CA</value></node>
+ <node>ASP:HA<value>ASP:HA</value></node>
+ <node>ASP:CB<value>ASP:CB</value></node>
+ <node>ASP:CG<value>ASP:CG</value></node>
+ <node>ASP:OD1<value>ASP:OD1</value></node>
+ <node>ASP:OD2<value>ASP:OD2</value></node>
+ <node>CYS:CA<value>CYS:CA</value></node>
+ <node>CYS:HA<value>CYS:HA</value></node>
+ <node>CYS:CB<value>CYS:CB</value></node>
+ <node>CYS:SG<value>CYS:SG</value></node>
+ <node>CYS:HG<value>CYS:HG</value></node>
+ <node>GLU:CA<value>GLU:CA</value></node>
+ <node>GLU:HA<value>GLU:HA</value></node>
+ <node>GLU:CB<value>GLU:CB</value></node>
+ <node>GLU:CG<value>GLU:CG</value></node>
+ <node>GLU:CD<value>GLU:CD</value></node>
+ <node>GLU:OE1<value>GLU:OE1</value></node>
+ <node>GLU:OE2<value>GLU:OE2</value></node>
+ <node>GLN:CA<value>GLN:CA</value></node>
+ <node>GLN:HA<value>GLN:HA</value></node>
+ <node>GLN:CB<value>GLN:CB</value></node>
+ <node>GLN:CG<value>GLN:CG</value></node>
+ <node>GLN:CD<value>GLN:CD</value></node>
+ <node>GLN:OE1<value>GLN:OE1</value></node>
+ <node>GLN:NE2<value>GLN:NE2</value></node>
+ <node>GLY:CA<value>GLY:CA</value></node>
+ <node>HIS:CA<value>HIS:CA</value></node>
+ <node>HIS:HA<value>HIS:HA</value></node>
+ <node>HIS:CB<value>HIS:CB</value></node>
+ <node>HIS:CG<value>HIS:CG</value></node>
+ <node>HIS:ND1<value>HIS:ND1</value></node>
+ <node>HIS:HD1<value>HIS:HD1</value></node>
+ <node>HIS:CE1<value>HIS:CE1</value></node>
+ <node>HIS:HE1<value>HIS:HE1</value></node>
+ <node>HIS:NE2<value>HIS:NE2</value></node>
+ <node>HIS:HE2<value>HIS:HE2</value></node>
+ <node>HIS:CD2<value>HIS:CD2</value></node>
+ <node>HIS:HD2<value>HIS:HD2</value></node>
+ <node>ILE:CA<value>ILE:CA</value></node>
+ <node>ILE:HA<value>ILE:HA</value></node>
+ <node>ILE:CB<value>ILE:CB</value></node>
+ <node>ILE:HB<value>ILE:HB</value></node>
+ <node>ILE:CG2<value>ILE:CG2</value></node>
+ <node>ILE:CG1<value>ILE:CG1</value></node>
+ <node>ILE:CD1<value>ILE:CD1</value></node>
+ <node>LEU:CA<value>LEU:CA</value></node>
+ <node>LEU:HA<value>LEU:HA</value></node>
+ <node>LEU:CB<value>LEU:CB</value></node>
+ <node>LEU:CG<value>LEU:CG</value></node>
+ <node>LEU:HG<value>LEU:HG</value></node>
+ <node>LEU:CD1<value>LEU:CD1</value></node>
+ <node>LEU:CD2<value>LEU:CD2</value></node>
+ <node>LYS:CA<value>LYS:CA</value></node>
+ <node>LYS:HA<value>LYS:HA</value></node>
+ <node>LYS:CB<value>LYS:CB</value></node>
+ <node>LYS:CG<value>LYS:CG</value></node>
+ <node>LYS:CD<value>LYS:CD</value></node>
+ <node>LYS:CE<value>LYS:CE</value></node>
+ <node>LYS:NZ<value>LYS:NZ</value></node>
+ <node>MET:CA<value>MET:CA</value></node>
+ <node>MET:HA<value>MET:HA</value></node>
+ <node>MET:CB<value>MET:CB</value></node>
+ <node>MET:CG<value>MET:CG</value></node>
+ <node>MET:SD<value>MET:SD</value></node>
+ <node>MET:CE<value>MET:CE</value></node>
+ <node>PHE:CA<value>PHE:CA</value></node>
+ <node>PHE:HA<value>PHE:HA</value></node>
+ <node>PHE:CB<value>PHE:CB</value></node>
+ <node>PHE:CG<value>PHE:CG</value></node>
+ <node>PHE:CD1<value>PHE:CD1</value></node>
+ <node>PHE:HD1<value>PHE:HD1</value></node>
+ <node>PHE:CE1<value>PHE:CE1</value></node>
+ <node>PHE:HE1<value>PHE:HE1</value></node>
+ <node>PHE:CZ<value>PHE:CZ</value></node>
+ <node>PHE:HZ<value>PHE:HZ</value></node>
+ <node>PHE:CE2<value>PHE:CE2</value></node>
+ <node>PHE:HE2<value>PHE:HE2</value></node>
+ <node>PHE:CD2<value>PHE:CD2</value></node>
+ <node>PHE:HD2<value>PHE:HD2</value></node>
+ <node>PRO:CA<value>PRO:CA</value></node>
+ <node>PRO:HA<value>PRO:HA</value></node>
+ <node>PRO:CD<value>PRO:CD</value></node>
+ <node>PRO:CG<value>PRO:CG</value></node>
+ <node>PRO:CB<value>PRO:CB</value></node>
+ <node>SER:CA<value>SER:CA</value></node>
+ <node>SER:HA<value>SER:HA</value></node>
+ <node>SER:CB<value>SER:CB</value></node>
+ <node>SER:OG<value>SER:OG</value></node>
+ <node>SER:HG<value>SER:HG</value></node>
+ <node>THR:CA<value>THR:CA</value></node>
+ <node>THR:HA<value>THR:HA</value></node>
+ <node>THR:CB<value>THR:CB</value></node>
+ <node>THR:HB<value>THR:HB</value></node>
+ <node>THR:CG2<value>THR:CG2</value></node>
+ <node>THR:OG1<value>THR:OG1</value></node>
+ <node>THR:HG1<value>THR:HG1</value></node>
+ <node>TRP:CA<value>TRP:CA</value></node>
+ <node>TRP:HA<value>TRP:HA</value></node>
+ <node>TRP:CB<value>TRP:CB</value></node>
+ <node>TRP:CG<value>TRP:CG</value></node>
+ <node>TRP:CD1<value>TRP:CD1</value></node>
+ <node>TRP:HD1<value>TRP:HD1</value></node>
+ <node>TRP:NE1<value>TRP:NE1</value></node>
+ <node>TRP:HE1<value>TRP:HE1</value></node>
+ <node>TRP:CE2<value>TRP:CE2</value></node>
+ <node>TRP:CZ2<value>TRP:CZ2</value></node>
+ <node>TRP:HZ2<value>TRP:HZ2</value></node>
+ <node>TRP:CH2<value>TRP:CH2</value></node>
+ <node>TRP:HH2<value>TRP:HH2</value></node>
+ <node>TRP:CZ3<value>TRP:CZ3</value></node>
+ <node>TRP:HZ3<value>TRP:HZ3</value></node>
+ <node>TRP:CE3<value>TRP:CE3</value></node>
+ <node>TRP:HE3<value>TRP:HE3</value></node>
+ <node>TRP:CD2<value>TRP:CD2</value></node>
+ <node>TYR:CA<value>TYR:CA</value></node>
+ <node>TYR:HA<value>TYR:HA</value></node>
+ <node>TYR:CB<value>TYR:CB</value></node>
+ <node>TYR:CG<value>TYR:CG</value></node>
+ <node>TYR:CD1<value>TYR:CD1</value></node>
+ <node>TYR:HD1<value>TYR:HD1</value></node>
+ <node>TYR:CE1<value>TYR:CE1</value></node>
+ <node>TYR:HE1<value>TYR:HE1</value></node>
+ <node>TYR:CZ<value>TYR:CZ</value></node>
+ <node>TYR:OH<value>TYR:OH</value></node>
+ <node>TYR:HH<value>TYR:HH</value></node>
+ <node>TYR:CE2<value>TYR:CE2</value></node>
+ <node>TYR:HE2<value>TYR:HE2</value></node>
+ <node>TYR:CD2<value>TYR:CD2</value></node>
+ <node>TYR:HD2<value>TYR:HD2</value></node>
+ <node>VAL:CA<value>VAL:CA</value></node>
+ <node>VAL:HA<value>VAL:HA</value></node>
+ <node>VAL:CB<value>VAL:CB</value></node>
+ <node>VAL:HB<value>VAL:HB</value></node>
+ <node>VAL:CG1<value>VAL:CG1</value></node>
+ <node>VAL:CG2<value>VAL:CG2</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.DNA.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,174 @@
+<node>DNA<value>PDB</value>
+ <node>C:P<value>C:P</value></node>
+ <node>DC:OP1<value>C:O1P</value></node>
+ <node>DC:OP2<value>C:O2P</value></node>
+ <node>DC:*<value>C:*</value></node>
+ <node>C:OP1<value>C:O1P</value></node>
+ <node>C:OP2<value>C:O2P</value></node>
+ <node>C:O5'<value>C:O5*</value></node>
+ <node>C:C5'<value>C:C5*</value></node>
+ <node>C:H5'<value>C:1H5*</value></node>
+ <node>C:H5''<value>C:2H5*</value></node>
+ <node>C:C4'<value>C:C4*</value></node>
+ <node>C:H4'<value>C:H4*</value></node>
+ <node>C:O4'<value>C:O4*</value></node>
+ <node>C:C1'<value>C:C1*</value></node>
+ <node>C:H1'<value>C:H1*</value></node>
+ <node>C:N1<value>C:N1</value></node>
+ <node>C:C6<value>C:C6</value></node>
+ <node>C:H6<value>C:H6</value></node>
+ <node>C:C5<value>C:C5</value></node>
+ <node>C:H5<value>C:H5</value></node>
+ <node>C:C4<value>C:C4</value></node>
+ <node>C:N4<value>C:N4</value></node>
+ <node>C:H41<value>C:1H4</value></node>
+ <node>C:H42<value>C:2H4</value></node>
+ <node>C:N3<value>C:N3</value></node>
+ <node>C:C2<value>C:C2</value></node>
+ <node>C:O2<value>C:O2</value></node>
+ <node>C:O2'<value>C:O2*</value></node>
+ <node>C:HO2'<value>C:HO3*</value></node>
+ <node>C:C3'<value>C:C3*</value></node>
+ <node>C:H3'<value>C:H3*</value></node>
+ <node>C:C2'<value>C:C2*</value></node>
+ <node>C:H2'<value>C:1H2*</value></node>
+ <node>C:H2''<value>C:2H2*</value></node>
+ <node>C:O3'<value>C:O3*</value></node>
+ <node>A:P<value>A:P</value></node>
+ <node>DA:OP1<value>A:O1P</value></node>
+ <node>DA:OP2<value>A:O2P</value></node>
+ <node>DA:*<value>A:*</value></node>
+ <node>A:OP1<value>A:O1P</value></node>
+ <node>A:OP2<value>A:O2P</value></node>
+ <node>A:O5'<value>A:O5*</value></node>
+ <node>A:C5'<value>A:C5*</value></node>
+ <node>A:H5'<value>A:1H5*</value></node>
+ <node>A:H5''<value>A:2H5*</value></node>
+ <node>A:C4'<value>A:C4*</value></node>
+ <node>A:H4'<value>A:H4*</value></node>
+ <node>A:O4'<value>A:O4*</value></node>
+ <node>A:C1'<value>A:C1*</value></node>
+ <node>A:H1'<value>A:H1*</value></node>
+ <node>A:N9<value>A:N9</value></node>
+ <node>A:C8<value>A:C8</value></node>
+ <node>A:H8<value>A:H8</value></node>
+ <node>A:N7<value>A:N7</value></node>
+ <node>A:C5<value>A:C5</value></node>
+ <node>A:C6<value>A:C6</value></node>
+ <node>A:N6<value>A:N6</value></node>
+ <node>A:H61<value>A:1H6</value></node>
+ <node>A:H62<value>A:2H6</value></node>
+ <node>A:N1<value>A:N1</value></node>
+ <node>A:C2<value>A:C2</value></node>
+ <node>A:H2<value>A:2H</value></node>
+ <node>A:N3<value>A:N3</value></node>
+ <node>A:C4<value>A:C4</value></node>
+ <node>A:C3'<value>A:C3*</value></node>
+ <node>A:H3'<value>A:H3*</value></node>
+ <node>A:C2'<value>A:C2*</value></node>
+ <node>A:H2'<value>A:1H2*</value></node>
+ <node>A:H2''<value>A:2H2*</value></node>
+ <node>A:O3'<value>A:O3*</value></node>
+ <node>U:P<value>U:P</value></node>
+ <node>U:OP1<value>U:O1P</value></node>
+ <node>U:OP2<value>U:O2P</value></node>
+ <node>U:O5'<value>U:O5*</value></node>
+ <node>U:C5'<value>U:C5*</value></node>
+ <node>U:H5'<value>U:1H5*</value></node>
+ <node>U:H5''<value>U:2H5*</value></node>
+ <node>U:C4'<value>U:C4*</value></node>
+ <node>U:H4'<value>U:H4*</value></node>
+ <node>U:O4'<value>U:O4*</value></node>
+ <node>U:C1'<value>U:C1*</value></node>
+ <node>U:H1'<value>U:H1*</value></node>
+ <node>U:N1<value>U:N1</value></node>
+ <node>U:C6<value>U:C6</value></node>
+ <node>U:H6<value>U:H6</value></node>
+ <node>U:C5<value>U:C5</value></node>
+ <node>U:C4<value>U:C4</value></node>
+ <node>U:O4<value>U:O4</value></node>
+ <node>U:N3<value>U:N3</value></node>
+ <node>U:H3<value>U:H3</value></node>
+ <node>U:C2<value>U:C2</value></node>
+ <node>U:O2<value>U:O2</value></node>
+ <node>U:O2'<value>U:O2*</value></node>
+ <node>U:HO2'<value>U:HO2*</value></node>
+ <node>U:C3'<value>U:C3*</value></node>
+ <node>U:H3'<value>U:H3*</value></node>
+ <node>U:C2'<value>U:C2*</value></node>
+ <node>U:H2'<value>U:1H2*</value></node>
+ <node>U:H2''<value>U:2H2*</value></node>
+ <node>U:O3'<value>U:O3*</value></node>
+
+ <node>T:P<value>T:P</value></node>
+ <node>DT:OP1<value>T:O1P</value></node>
+ <node>DT:OP2<value>T:O2P</value></node>
+ <node>DT:*<value>T:*</value></node>
+ <node>T:OP1<value>T:O1P</value></node>
+ <node>T:OP2<value>T:O2P</value></node>
+ <node>T:O5'<value>T:O5*</value></node>
+ <node>T:C5'<value>T:C5*</value></node>
+ <node>T:H5'<value>T:1H5*</value></node>
+ <node>T:H5''<value>T:2H5*</value></node>
+ <node>T:C4'<value>T:C4*</value></node>
+ <node>T:H4'<value>T:H4*</value></node>
+ <node>T:O4'<value>T:O4*</value></node>
+ <node>T:C1'<value>T:C1*</value></node>
+ <node>T:H1'<value>T:H1*</value></node>
+ <node>T:N1<value>T:N1</value></node>
+ <node>T:C6<value>T:C6</value></node>
+ <node>T:H6<value>T:H6</value></node>
+ <node>T:C5<value>T:C5</value></node>
+ <node>T:C7<value>T:C5M</value></node>
+ <node>T:H71<value>T:1H5M</value></node>
+ <node>T:H72<value>T:2H5M</value></node>
+ <node>T:H73<value>T:3H5M</value></node>
+ <node>T:C4<value>T:C4</value></node>
+ <node>T:O4<value>T:O4</value></node>
+ <node>T:N3<value>T:N3</value></node>
+ <node>T:C2<value>T:C2</value></node>
+ <node>T:O2<value>T:O2</value></node>
+ <node>T:C3'<value>T:C3*</value></node>
+ <node>T:H3'<value>T:H3*</value></node>
+ <node>T:C2'<value>T:C2*</value></node>
+ <node>T:H2'<value>T:1H2*</value></node>
+ <node>T:H2''<value>T:2H2*</value></node>
+ <node>T:O3'<value>T:O3*</value></node>
+ <node>T:H3<value>T:3H</value></node>
+ <node>G:P<value>G:P</value></node>
+ <node>DG:OP1<value>G:O1P</value></node>
+ <node>DG:OP2<value>G:O2P</value></node>
+ <node>DG:*<value>G:*</value></node>
+ <node>G:OP1<value>G:O1P</value></node>
+ <node>G:OP2<value>G:O2P</value></node>
+ <node>G:O5'<value>G:O5*</value></node>
+ <node>G:C5'<value>G:C5*</value></node>
+ <node>G:H5'<value>G:1H5*</value></node>
+ <node>G:H5''<value>G:2H5*</value></node>
+ <node>G:C4'<value>G:C4*</value></node>
+ <node>G:H4'<value>G:H4*</value></node>
+ <node>G:O4'<value>G:O4*</value></node>
+ <node>G:C1'<value>G:C1*</value></node>
+ <node>G:H1'<value>G:H1*</value></node>
+ <node>G:N9<value>G:N9</value></node>
+ <node>G:C8<value>G:C8</value></node>
+ <node>G:H8<value>G:H8</value></node>
+ <node>G:N7<value>G:N7</value></node>
+ <node>G:C5<value>G:C5</value></node>
+ <node>G:C6<value>G:C6</value></node>
+ <node>G:O6<value>G:O6</value></node>
+ <node>G:N1<value>G:N1</value></node>
+ <node>G:H1<value>G:1H</value></node>
+ <node>G:C2<value>G:C2</value></node>
+ <node>G:N2<value>G:N2</value></node>
+ <node>G:H21<value>G:1H2</value></node>
+ <node>G:H22<value>G:2H2</value></node>
+ <node>G:N3<value>G:N3</value></node>
+ <node>G:C4<value>G:C4</value></node>
+ <node>G:C3'<value>G:C3*</value></node>
+ <node>G:H3'<value>G:H3*</value></node>
+ <node>G:C2'<value>G:C2*</value></node>
+ <node>G:H2'<value>G:1H2*</value></node>
+ <node>G:H2''<value>G:2H2*</value></node>
+ <node>G:O3'<value>G:O3*</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.Discover.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,255 @@
+<node>Discover<value>PDB</value>
+ <node>*:H1<value>*:1H</value></node>
+ <node>*:H2<value>*:2H</value></node>
+ <node>*:H3<value>*:3H</value></node>
+ <node>*:N<value>*:N</value></node>
+ <node>*:O<value>*:O</value></node>
+ <node>*:C<value>*:C</value></node>
+ <node>*:HN<value>*:H</value></node>
+ <node>ALA:CA<value>ALA:CA</value></node>
+ <node>ALA:HA<value>ALA:HA</value></node>
+ <node>ALA:CB<value>ALA:CB</value></node>
+ <node>ALA:HB1<value>ALA:1HB</value></node>
+ <node>ALA:HB2<value>ALA:2HB</value></node>
+ <node>ALA:HB3<value>ALA:3HB</value></node>
+ <node>ARG:CA<value>ARG:CA</value></node>
+ <node>ARG:HA<value>ARG:HA</value></node>
+ <node>ARG:CB<value>ARG:CB</value></node>
+ <node>ARG:HB1<value>ARG:1HB</value></node>
+ <node>ARG:HB2<value>ARG:2HB</value></node>
+ <node>ARG:CG<value>ARG:CG</value></node>
+ <node>ARG:HG1<value>ARG:1HG</value></node>
+ <node>ARG:HG2<value>ARG:2HG</value></node>
+ <node>ARG:CD<value>ARG:CD</value></node>
+ <node>ARG:HD1<value>ARG:1HD</value></node>
+ <node>ARG:HD2<value>ARG:2HD</value></node>
+ <node>ARG:NE<value>ARG:NE</value></node>
+ <node>ARG:HE<value>ARG:HE</value></node>
+ <node>ARG:CZ<value>ARG:CZ</value></node>
+ <node>ARG:NH1<value>ARG:NH1</value></node>
+ <node>ARG:HH11<value>ARG:1HH1</value></node>
+ <node>ARG:HH12<value>ARG:2HH1</value></node>
+ <node>ARG:NH2<value>ARG:NH2</value></node>
+ <node>ARG:HH21<value>ARG:1HH2</value></node>
+ <node>ARG:HH22<value>ARG:2HH2</value></node>
+ <node>ASN:CA<value>ASN:CA</value></node>
+ <node>ASN:HA<value>ASN:HA</value></node>
+ <node>ASN:CB<value>ASN:CB</value></node>
+ <node>ASN:HB1<value>ASN:1HB</value></node>
+ <node>ASN:HB2<value>ASN:2HB</value></node>
+ <node>ASN:CG<value>ASN:CG</value></node>
+ <node>ASN:OD1<value>ASN:OD1</value></node>
+ <node>ASN:ND2<value>ASN:ND2</value></node>
+ <node>ASN:HD21<value>ASN:1HD2</value></node>
+ <node>ASN:HD22<value>ASN:2HD2</value></node>
+ <node>ASP:CA<value>ASP:CA</value></node>
+ <node>ASP:HA<value>ASP:HA</value></node>
+ <node>ASP:CB<value>ASP:CB</value></node>
+ <node>ASP:HB1<value>ASP:1HB</value></node>
+ <node>ASP:HB2<value>ASP:2HB</value></node>
+ <node>ASP:CG<value>ASP:CG</value></node>
+ <node>ASP:OD1<value>ASP:OD1</value></node>
+ <node>ASP:OD2<value>ASP:OD2</value></node>
+ <node>CYS:CA<value>CYS:CA</value></node>
+ <node>CYS:HA<value>CYS:HA</value></node>
+ <node>CYS:CB<value>CYS:CB</value></node>
+ <node>CYS:HB1<value>CYS:1HB</value></node>
+ <node>CYS:HB2<value>CYS:2HB</value></node>
+ <node>CYS:SG<value>CYS:SG</value></node>
+ <node>CYS:HG<value>CYS:HG</value></node>
+ <node>GLU:CA<value>GLU:CA</value></node>
+ <node>GLU:HA<value>GLU:HA</value></node>
+ <node>GLU:CB<value>GLU:CB</value></node>
+ <node>GLU:HB1<value>GLU:1HB</value></node>
+ <node>GLU:HB2<value>GLU:2HB</value></node>
+ <node>GLU:CG<value>GLU:CG</value></node>
+ <node>GLU:HG1<value>GLU:1HG</value></node>
+ <node>GLU:HG2<value>GLU:2HG</value></node>
+ <node>GLU:CD<value>GLU:CD</value></node>
+ <node>GLU:OE1<value>GLU:OE1</value></node>
+ <node>GLU:OE2<value>GLU:OE2</value></node>
+ <node>GLN:CA<value>GLN:CA</value></node>
+ <node>GLN:HA<value>GLN:HA</value></node>
+ <node>GLN:CB<value>GLN:CB</value></node>
+ <node>GLN:HB1<value>GLN:1HB</value></node>
+ <node>GLN:HB2<value>GLN:2HB</value></node>
+ <node>GLN:CG<value>GLN:CG</value></node>
+ <node>GLN:HG1<value>GLN:1HG</value></node>
+ <node>GLN:HG2<value>GLN:2HG</value></node>
+ <node>GLN:CD<value>GLN:CD</value></node>
+ <node>GLN:OE1<value>GLN:OE1</value></node>
+ <node>GLN:NE2<value>GLN:NE2</value></node>
+ <node>GLN:HE21<value>GLN:1HE2</value></node>
+ <node>GLN:HE22<value>GLN:2HE2</value></node>
+ <node>GLY:CA<value>GLY:CA</value></node>
+ <node>GLY:HA1<value>GLY:1HA</value></node>
+ <node>GLY:HA2<value>GLY:2HA</value></node>
+ <node>HIS:CA<value>HIS:CA</value></node>
+ <node>HIS:HA<value>HIS:HA</value></node>
+ <node>HIS:CB<value>HIS:CB</value></node>
+ <node>HIS:HB1<value>HIS:1HB</value></node>
+ <node>HIS:HB2<value>HIS:2HB</value></node>
+ <node>HIS:CG<value>HIS:CG</value></node>
+ <node>HIS:ND1<value>HIS:ND1</value></node>
+ <node>HIS:HD1<value>HIS:HD1</value></node>
+ <node>HIS:CE1<value>HIS:CE1</value></node>
+ <node>HIS:HE1<value>HIS:HE1</value></node>
+ <node>HIS:NE2<value>HIS:NE2</value></node>
+ <node>HIS:HE2<value>HIS:HE2</value></node>
+ <node>HIS:CD2<value>HIS:CD2</value></node>
+ <node>HIS:HD2<value>HIS:HD2</value></node>
+ <node>ILE:CA<value>ILE:CA</value></node>
+ <node>ILE:HA<value>ILE:HA</value></node>
+ <node>ILE:CB<value>ILE:CB</value></node>
+ <node>ILE:HB<value>ILE:HB</value></node>
+ <node>ILE:CG2<value>ILE:CG2</value></node>
+ <node>ILE:HG21<value>ILE:1HG2</value></node>
+ <node>ILE:HG22<value>ILE:2HG2</value></node>
+ <node>ILE:HG23<value>ILE:3HG2</value></node>
+ <node>ILE:CG1<value>ILE:CG1</value></node>
+ <node>ILE:HG11<value>ILE:1HG1</value></node>
+ <node>ILE:HG12<value>ILE:2HG1</value></node>
+ <node>ILE:CD1<value>ILE:CD1</value></node>
+ <node>ILE:HD11<value>ILE:1HD1</value></node>
+ <node>ILE:HD12<value>ILE:2HD1</value></node>
+ <node>ILE:HD13<value>ILE:3HD1</value></node>
+ <node>LEU:CA<value>LEU:CA</value></node>
+ <node>LEU:HA<value>LEU:HA</value></node>
+ <node>LEU:CB<value>LEU:CB</value></node>
+ <node>LEU:HB1<value>LEU:1HB</value></node>
+ <node>LEU:HB2<value>LEU:2HB</value></node>
+ <node>LEU:CG<value>LEU:CG</value></node>
+ <node>LEU:HG<value>LEU:HG</value></node>
+ <node>LEU:CD1<value>LEU:CD1</value></node>
+ <node>LEU:HD11<value>LEU:1HD1</value></node>
+ <node>LEU:HD12<value>LEU:2HD1</value></node>
+ <node>LEU:HD13<value>LEU:3HD1</value></node>
+ <node>LEU:CD2<value>LEU:CD2</value></node>
+ <node>LEU:HD21<value>LEU:1HD2</value></node>
+ <node>LEU:HD22<value>LEU:2HD2</value></node>
+ <node>LEU:HD23<value>LEU:3HD2</value></node>
+ <node>LYS:CA<value>LYS:CA</value></node>
+ <node>LYS:HA<value>LYS:HA</value></node>
+ <node>LYS:CB<value>LYS:CB</value></node>
+ <node>LYS:HB1<value>LYS:1HB</value></node>
+ <node>LYS:HB2<value>LYS:2HB</value></node>
+ <node>LYS:CG<value>LYS:CG</value></node>
+ <node>LYS:HG1<value>LYS:1HG</value></node>
+ <node>LYS:HG2<value>LYS:2HG</value></node>
+ <node>LYS:CD<value>LYS:CD</value></node>
+ <node>LYS:HD1<value>LYS:1HD</value></node>
+ <node>LYS:HD2<value>LYS:2HD</value></node>
+ <node>LYS:CE<value>LYS:CE</value></node>
+ <node>LYS:HE1<value>LYS:1HE</value></node>
+ <node>LYS:HE2<value>LYS:2HE</value></node>
+ <node>LYS:NZ<value>LYS:NZ</value></node>
+ <node>LYS:HZ1<value>LYS:1HZ</value></node>
+ <node>LYS:HZ2<value>LYS:2HZ</value></node>
+ <node>LYS:HZ3<value>LYS:3HZ</value></node>
+ <node>MET:CA<value>MET:CA</value></node>
+ <node>MET:HA<value>MET:HA</value></node>
+ <node>MET:CB<value>MET:CB</value></node>
+ <node>MET:HB1<value>MET:1HB</value></node>
+ <node>MET:HB2<value>MET:2HB</value></node>
+ <node>MET:CG<value>MET:CG</value></node>
+ <node>MET:HG1<value>MET:1HG</value></node>
+ <node>MET:HG2<value>MET:2HG</value></node>
+ <node>MET:SD<value>MET:SD</value></node>
+ <node>MET:CE<value>MET:CE</value></node>
+ <node>MET:HE1<value>MET:1HE</value></node>
+ <node>MET:HE2<value>MET:2HE</value></node>
+ <node>MET:HE3<value>MET:3HE</value></node>
+ <node>PHE:CA<value>PHE:CA</value></node>
+ <node>PHE:HA<value>PHE:HA</value></node>
+ <node>PHE:CB<value>PHE:CB</value></node>
+ <node>PHE:HB1<value>PHE:1HB</value></node>
+ <node>PHE:HB2<value>PHE:2HB</value></node>
+ <node>PHE:CG<value>PHE:CG</value></node>
+ <node>PHE:CD1<value>PHE:CD1</value></node>
+ <node>PHE:HD1<value>PHE:HD1</value></node>
+ <node>PHE:CE1<value>PHE:CE1</value></node>
+ <node>PHE:HE1<value>PHE:HE1</value></node>
+ <node>PHE:CZ<value>PHE:CZ</value></node>
+ <node>PHE:HZ<value>PHE:HZ</value></node>
+ <node>PHE:CE2<value>PHE:CE2</value></node>
+ <node>PHE:HE2<value>PHE:HE2</value></node>
+ <node>PHE:CD2<value>PHE:CD2</value></node>
+ <node>PHE:HD2<value>PHE:HD2</value></node>
+ <node>PRO:CA<value>PRO:CA</value></node>
+ <node>PRO:HA<value>PRO:HA</value></node>
+ <node>PRO:CD<value>PRO:CD</value></node>
+ <node>PRO:HD1<value>PRO:1HD</value></node>
+ <node>PRO:HD2<value>PRO:2HD</value></node>
+ <node>PRO:CG<value>PRO:CG</value></node>
+ <node>PRO:HG1<value>PRO:1HG</value></node>
+ <node>PRO:HG2<value>PRO:2HG</value></node>
+ <node>PRO:CB<value>PRO:CB</value></node>
+ <node>PRO:HB1<value>PRO:1HB</value></node>
+ <node>PRO:HB2<value>PRO:2HB</value></node>
+ <node>SER:CA<value>SER:CA</value></node>
+ <node>SER:HA<value>SER:HA</value></node>
+ <node>SER:CB<value>SER:CB</value></node>
+ <node>SER:HB1<value>SER:1HB</value></node>
+ <node>SER:HB2<value>SER:2HB</value></node>
+ <node>SER:OG<value>SER:OG</value></node>
+ <node>SER:HG<value>SER:HG</value></node>
+ <node>THR:CA<value>THR:CA</value></node>
+ <node>THR:HA<value>THR:HA</value></node>
+ <node>THR:CB<value>THR:CB</value></node>
+ <node>THR:HB<value>THR:HB</value></node>
+ <node>THR:CG2<value>THR:CG2</value></node>
+ <node>THR:HG21<value>THR:1HG2</value></node>
+ <node>THR:HG22<value>THR:2HG2</value></node>
+ <node>THR:HG23<value>THR:3HG2</value></node>
+ <node>THR:OG1<value>THR:OG1</value></node>
+ <node>THR:HG1<value>THR:HG1</value></node>
+ <node>TRP:CA<value>TRP:CA</value></node>
+ <node>TRP:HA<value>TRP:HA</value></node>
+ <node>TRP:CB<value>TRP:CB</value></node>
+ <node>TRP:HB1<value>TRP:1HB</value></node>
+ <node>TRP:HB2<value>TRP:2HB</value></node>
+ <node>TRP:CG<value>TRP:CG</value></node>
+ <node>TRP:CD1<value>TRP:CD1</value></node>
+ <node>TRP:HD1<value>TRP:HD1</value></node>
+ <node>TRP:NE1<value>TRP:NE1</value></node>
+ <node>TRP:HE1<value>TRP:HE1</value></node>
+ <node>TRP:CE2<value>TRP:CE2</value></node>
+ <node>TRP:CZ2<value>TRP:CZ2</value></node>
+ <node>TRP:HZ2<value>TRP:HZ2</value></node>
+ <node>TRP:CH2<value>TRP:CH2</value></node>
+ <node>TRP:HH2<value>TRP:HH2</value></node>
+ <node>TRP:CZ3<value>TRP:CZ3</value></node>
+ <node>TRP:HZ3<value>TRP:HZ3</value></node>
+ <node>TRP:CE3<value>TRP:CE3</value></node>
+ <node>TRP:HE3<value>TRP:HE3</value></node>
+ <node>TRP:CD2<value>TRP:CD2</value></node>
+ <node>TYR:CA<value>TYR:CA</value></node>
+ <node>TYR:HA<value>TYR:HA</value></node>
+ <node>TYR:CB<value>TYR:CB</value></node>
+ <node>TYR:HB1<value>TYR:1HB</value></node>
+ <node>TYR:HB2<value>TYR:2HB</value></node>
+ <node>TYR:CG<value>TYR:CG</value></node>
+ <node>TYR:CD1<value>TYR:CD1</value></node>
+ <node>TYR:HD1<value>TYR:HD1</value></node>
+ <node>TYR:CE1<value>TYR:CE1</value></node>
+ <node>TYR:HE1<value>TYR:HE1</value></node>
+ <node>TYR:CZ<value>TYR:CZ</value></node>
+ <node>TYR:OH<value>TYR:OH</value></node>
+ <node>TYR:HH<value>TYR:HH</value></node>
+ <node>TYR:CE2<value>TYR:CE2</value></node>
+ <node>TYR:HE2<value>TYR:HE2</value></node>
+ <node>TYR:CD2<value>TYR:CD2</value></node>
+ <node>TYR:HD2<value>TYR:HD2</value></node>
+ <node>VAL:CA<value>VAL:CA</value></node>
+ <node>VAL:HA<value>VAL:HA</value></node>
+ <node>VAL:CB<value>VAL:CB</value></node>
+ <node>VAL:HB<value>VAL:HB</value></node>
+ <node>VAL:CG1<value>VAL:CG1</value></node>
+ <node>VAL:HG11<value>VAL:1HG1</value></node>
+ <node>VAL:HG12<value>VAL:2HG1</value></node>
+ <node>VAL:HG13<value>VAL:3HG1</value></node>
+ <node>VAL:CG2<value>VAL:CG2</value></node>
+ <node>VAL:HG21<value>VAL:1HG2</value></node>
+ <node>VAL:HG22<value>VAL:2HG2</value></node>
+ <node>VAL:HG23<value>VAL:3HG2</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.Star.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,261 @@
+<node>Star<value>PDB</value>
+ <node>*:H1<value>*:1H</value></node>
+ <node>*:H2<value>*:2H</value></node>
+ <node>*:H3<value>*:3H</value></node>
+ <node>*:HT1<value>*:1H</value></node>
+ <node>*:HT2<value>*:2H</value></node>
+ <node>*:HT3<value>*:3H</value></node>
+ <node>*:OT1<value>*:O</value></node>
+ <node>*:OT2<value>*:OXT</value></node>
+ <node>*:N<value>*:N</value></node>
+ <node>*:O<value>*:O</value></node>
+ <node>*:C<value>*:C</value></node>
+ <node>*:HN<value>*:H</value></node>
+ <node>*:H<value>*:H</value></node>
+ <node>ALA:CA<value>ALA:CA</value></node>
+ <node>ALA:HA<value>ALA:HA</value></node>
+ <node>ALA:CB<value>ALA:CB</value></node>
+ <node>ALA:HB1<value>ALA:1HB</value></node>
+ <node>ALA:HB2<value>ALA:2HB</value></node>
+ <node>ALA:HB3<value>ALA:3HB</value></node>
+ <node>ARG:CA<value>ARG:CA</value></node>
+ <node>ARG:HA<value>ARG:HA</value></node>
+ <node>ARG:CB<value>ARG:CB</value></node>
+ <node>ARG:HB2<value>ARG:1HB</value></node>
+ <node>ARG:HB3<value>ARG:2HB</value></node>
+ <node>ARG:CG<value>ARG:CG</value></node>
+ <node>ARG:HG2<value>ARG:1HG</value></node>
+ <node>ARG:HG3<value>ARG:2HG</value></node>
+ <node>ARG:CD<value>ARG:CD</value></node>
+ <node>ARG:HD2<value>ARG:1HD</value></node>
+ <node>ARG:HD3<value>ARG:2HD</value></node>
+ <node>ARG:NE<value>ARG:NE</value></node>
+ <node>ARG:HE<value>ARG:HE</value></node>
+ <node>ARG:CZ<value>ARG:CZ</value></node>
+ <node>ARG:NH1<value>ARG:NH1</value></node>
+ <node>ARG:HH11<value>ARG:1HH1</value></node>
+ <node>ARG:HH12<value>ARG:2HH1</value></node>
+ <node>ARG:NH2<value>ARG:NH2</value></node>
+ <node>ARG:HH21<value>ARG:1HH2</value></node>
+ <node>ARG:HH22<value>ARG:2HH2</value></node>
+ <node>ASN:CA<value>ASN:CA</value></node>
+ <node>ASN:HA<value>ASN:HA</value></node>
+ <node>ASN:CB<value>ASN:CB</value></node>
+ <node>ASN:HB2<value>ASN:1HB</value></node>
+ <node>ASN:HB3<value>ASN:2HB</value></node>
+ <node>ASN:CG<value>ASN:CG</value></node>
+ <node>ASN:OD1<value>ASN:OD1</value></node>
+ <node>ASN:ND2<value>ASN:ND2</value></node>
+ <node>ASN:HD21<value>ASN:1HD2</value></node>
+ <node>ASN:HD22<value>ASN:2HD2</value></node>
+ <node>ASP:CA<value>ASP:CA</value></node>
+ <node>ASP:HA<value>ASP:HA</value></node>
+ <node>ASP:CB<value>ASP:CB</value></node>
+ <node>ASP:HB2<value>ASP:1HB</value></node>
+ <node>ASP:HB3<value>ASP:2HB</value></node>
+ <node>ASP:CG<value>ASP:CG</value></node>
+ <node>ASP:OD1<value>ASP:OD1</value></node>
+ <node>ASP:OD2<value>ASP:OD2</value></node>
+ <node>CYS:CA<value>CYS:CA</value></node>
+ <node>CYS:HA<value>CYS:HA</value></node>
+ <node>CYS:CB<value>CYS:CB</value></node>
+ <node>CYS:HB2<value>CYS:1HB</value></node>
+ <node>CYS:HB3<value>CYS:2HB</value></node>
+ <node>CYS:SG<value>CYS:SG</value></node>
+ <node>CYS:HG<value>CYS:HG</value></node>
+ <node>GLU:CA<value>GLU:CA</value></node>
+ <node>GLU:HA<value>GLU:HA</value></node>
+ <node>GLU:CB<value>GLU:CB</value></node>
+ <node>GLU:HB2<value>GLU:1HB</value></node>
+ <node>GLU:HB3<value>GLU:2HB</value></node>
+ <node>GLU:CG<value>GLU:CG</value></node>
+ <node>GLU:HG2<value>GLU:1HG</value></node>
+ <node>GLU:HG3<value>GLU:2HG</value></node>
+ <node>GLU:CD<value>GLU:CD</value></node>
+ <node>GLU:OE1<value>GLU:OE1</value></node>
+ <node>GLU:OE2<value>GLU:OE2</value></node>
+ <node>GLN:CA<value>GLN:CA</value></node>
+ <node>GLN:HA<value>GLN:HA</value></node>
+ <node>GLN:CB<value>GLN:CB</value></node>
+ <node>GLN:HB2<value>GLN:1HB</value></node>
+ <node>GLN:HB3<value>GLN:2HB</value></node>
+ <node>GLN:CG<value>GLN:CG</value></node>
+ <node>GLN:HG2<value>GLN:1HG</value></node>
+ <node>GLN:HG3<value>GLN:2HG</value></node>
+ <node>GLN:CD<value>GLN:CD</value></node>
+ <node>GLN:OE1<value>GLN:OE1</value></node>
+ <node>GLN:NE2<value>GLN:NE2</value></node>
+ <node>GLN:HE21<value>GLN:1HE2</value></node>
+ <node>GLN:HE22<value>GLN:2HE2</value></node>
+ <node>GLY:CA<value>GLY:CA</value></node>
+ <node>GLY:HA2<value>GLY:1HA</value></node>
+ <node>GLY:HA3<value>GLY:2HA</value></node>
+ <node>HIS:CA<value>HIS:CA</value></node>
+ <node>HIS:HA<value>HIS:HA</value></node>
+ <node>HIS:CB<value>HIS:CB</value></node>
+ <node>HIS:HB2<value>HIS:1HB</value></node>
+ <node>HIS:HB3<value>HIS:2HB</value></node>
+ <node>HIS:CG<value>HIS:CG</value></node>
+ <node>HIS:ND1<value>HIS:ND1</value></node>
+ <node>HIS:HD1<value>HIS:HD1</value></node>
+ <node>HIS:CE1<value>HIS:CE1</value></node>
+ <node>HIS:HE1<value>HIS:HE1</value></node>
+ <node>HIS:NE2<value>HIS:NE2</value></node>
+ <node>HIS:HE2<value>HIS:HE2</value></node>
+ <node>HIS:CD2<value>HIS:CD2</value></node>
+ <node>HIS:HD2<value>HIS:HD2</value></node>
+ <node>ILE:CA<value>ILE:CA</value></node>
+ <node>ILE:HA<value>ILE:HA</value></node>
+ <node>ILE:CB<value>ILE:CB</value></node>
+ <node>ILE:HB<value>ILE:HB</value></node>
+ <node>ILE:CG2<value>ILE:CG2</value></node>
+ <node>ILE:HG21<value>ILE:1HG2</value></node>
+ <node>ILE:HG22<value>ILE:2HG2</value></node>
+ <node>ILE:HG23<value>ILE:3HG2</value></node>
+ <node>ILE:CG1<value>ILE:CG1</value></node>
+ <node>ILE:HG12<value>ILE:1HG1</value></node>
+ <node>ILE:HG13<value>ILE:2HG1</value></node>
+ <node>ILE:CD1<value>ILE:CD1</value></node>
+ <node>ILE:HD11<value>ILE:1HD1</value></node>
+ <node>ILE:HD12<value>ILE:2HD1</value></node>
+ <node>ILE:HD13<value>ILE:3HD1</value></node>
+ <node>LEU:CA<value>LEU:CA</value></node>
+ <node>LEU:HA<value>LEU:HA</value></node>
+ <node>LEU:CB<value>LEU:CB</value></node>
+ <node>LEU:HB2<value>LEU:1HB</value></node>
+ <node>LEU:HB3<value>LEU:2HB</value></node>
+ <node>LEU:CG<value>LEU:CG</value></node>
+ <node>LEU:HG<value>LEU:HG</value></node>
+ <node>LEU:CD1<value>LEU:CD1</value></node>
+ <node>LEU:HD11<value>LEU:1HD1</value></node>
+ <node>LEU:HD12<value>LEU:2HD1</value></node>
+ <node>LEU:HD13<value>LEU:3HD1</value></node>
+ <node>LEU:CD2<value>LEU:CD2</value></node>
+ <node>LEU:HD21<value>LEU:1HD2</value></node>
+ <node>LEU:HD22<value>LEU:2HD2</value></node>
+ <node>LEU:HD23<value>LEU:3HD2</value></node>
+ <node>LYS:CA<value>LYS:CA</value></node>
+ <node>LYS:HA<value>LYS:HA</value></node>
+ <node>LYS:CB<value>LYS:CB</value></node>
+ <node>LYS:HB2<value>LYS:1HB</value></node>
+ <node>LYS:HB3<value>LYS:2HB</value></node>
+ <node>LYS:CG<value>LYS:CG</value></node>
+ <node>LYS:HG2<value>LYS:1HG</value></node>
+ <node>LYS:HG3<value>LYS:2HG</value></node>
+ <node>LYS:CD<value>LYS:CD</value></node>
+ <node>LYS:HD2<value>LYS:1HD</value></node>
+ <node>LYS:HD3<value>LYS:2HD</value></node>
+ <node>LYS:CE<value>LYS:CE</value></node>
+ <node>LYS:HE2<value>LYS:1HE</value></node>
+ <node>LYS:HE3<value>LYS:2HE</value></node>
+ <node>LYS:NZ<value>LYS:NZ</value></node>
+ <node>LYS:HZ1<value>LYS:1HZ</value></node>
+ <node>LYS:HZ2<value>LYS:2HZ</value></node>
+ <node>LYS:HZ3<value>LYS:3HZ</value></node>
+ <node>MET:CA<value>MET:CA</value></node>
+ <node>MET:HA<value>MET:HA</value></node>
+ <node>MET:CB<value>MET:CB</value></node>
+ <node>MET:HB2<value>MET:1HB</value></node>
+ <node>MET:HB3<value>MET:2HB</value></node>
+ <node>MET:CG<value>MET:CG</value></node>
+ <node>MET:HG2<value>MET:1HG</value></node>
+ <node>MET:HG3<value>MET:2HG</value></node>
+ <node>MET:SD<value>MET:SD</value></node>
+ <node>MET:CE<value>MET:CE</value></node>
+ <node>MET:HE1<value>MET:1HE</value></node>
+ <node>MET:HE2<value>MET:2HE</value></node>
+ <node>MET:HE3<value>MET:3HE</value></node>
+ <node>PHE:CA<value>PHE:CA</value></node>
+ <node>PHE:HA<value>PHE:HA</value></node>
+ <node>PHE:CB<value>PHE:CB</value></node>
+ <node>PHE:HB2<value>PHE:1HB</value></node>
+ <node>PHE:HB3<value>PHE:2HB</value></node>
+ <node>PHE:CG<value>PHE:CG</value></node>
+ <node>PHE:CD1<value>PHE:CD1</value></node>
+ <node>PHE:HD1<value>PHE:HD1</value></node>
+ <node>PHE:CE1<value>PHE:CE1</value></node>
+ <node>PHE:HE1<value>PHE:HE1</value></node>
+ <node>PHE:CZ<value>PHE:CZ</value></node>
+ <node>PHE:HZ<value>PHE:HZ</value></node>
+ <node>PHE:CE2<value>PHE:CE2</value></node>
+ <node>PHE:HE2<value>PHE:HE2</value></node>
+ <node>PHE:CD2<value>PHE:CD2</value></node>
+ <node>PHE:HD2<value>PHE:HD2</value></node>
+ <node>PRO:CA<value>PRO:CA</value></node>
+ <node>PRO:HA<value>PRO:HA</value></node>
+ <node>PRO:CD<value>PRO:CD</value></node>
+ <node>PRO:HD2<value>PRO:1HD</value></node>
+ <node>PRO:HD3<value>PRO:2HD</value></node>
+ <node>PRO:CG<value>PRO:CG</value></node>
+ <node>PRO:HG2<value>PRO:1HG</value></node>
+ <node>PRO:HG3<value>PRO:2HG</value></node>
+ <node>PRO:CB<value>PRO:CB</value></node>
+ <node>PRO:HB2<value>PRO:1HB</value></node>
+ <node>PRO:HB3<value>PRO:2HB</value></node>
+ <node>SER:CA<value>SER:CA</value></node>
+ <node>SER:HA<value>SER:HA</value></node>
+ <node>SER:CB<value>SER:CB</value></node>
+ <node>SER:HB2<value>SER:1HB</value></node>
+ <node>SER:HB3<value>SER:2HB</value></node>
+ <node>SER:OG<value>SER:OG</value></node>
+ <node>SER:HG<value>SER:HG</value></node>
+ <node>THR:CA<value>THR:CA</value></node>
+ <node>THR:HA<value>THR:HA</value></node>
+ <node>THR:CB<value>THR:CB</value></node>
+ <node>THR:HB<value>THR:HB</value></node>
+ <node>THR:CG2<value>THR:CG2</value></node>
+ <node>THR:HG21<value>THR:1HG2</value></node>
+ <node>THR:HG22<value>THR:2HG2</value></node>
+ <node>THR:HG23<value>THR:3HG2</value></node>
+ <node>THR:OG1<value>THR:OG1</value></node>
+ <node>THR:HG1<value>THR:HG1</value></node>
+ <node>TRP:CA<value>TRP:CA</value></node>
+ <node>TRP:HA<value>TRP:HA</value></node>
+ <node>TRP:CB<value>TRP:CB</value></node>
+ <node>TRP:HB2<value>TRP:1HB</value></node>
+ <node>TRP:HB3<value>TRP:2HB</value></node>
+ <node>TRP:CG<value>TRP:CG</value></node>
+ <node>TRP:CD1<value>TRP:CD1</value></node>
+ <node>TRP:HD1<value>TRP:HD1</value></node>
+ <node>TRP:NE1<value>TRP:NE1</value></node>
+ <node>TRP:HE1<value>TRP:HE1</value></node>
+ <node>TRP:CE2<value>TRP:CE2</value></node>
+ <node>TRP:CZ2<value>TRP:CZ2</value></node>
+ <node>TRP:HZ2<value>TRP:HZ2</value></node>
+ <node>TRP:CH2<value>TRP:CH2</value></node>
+ <node>TRP:HH2<value>TRP:HH2</value></node>
+ <node>TRP:CZ3<value>TRP:CZ3</value></node>
+ <node>TRP:HZ3<value>TRP:HZ3</value></node>
+ <node>TRP:CE3<value>TRP:CE3</value></node>
+ <node>TRP:HE3<value>TRP:HE3</value></node>
+ <node>TRP:CD2<value>TRP:CD2</value></node>
+ <node>TYR:CA<value>TYR:CA</value></node>
+ <node>TYR:HA<value>TYR:HA</value></node>
+ <node>TYR:CB<value>TYR:CB</value></node>
+ <node>TYR:HB2<value>TYR:1HB</value></node>
+ <node>TYR:HB3<value>TYR:2HB</value></node>
+ <node>TYR:CG<value>TYR:CG</value></node>
+ <node>TYR:CD1<value>TYR:CD1</value></node>
+ <node>TYR:HD1<value>TYR:HD1</value></node>
+ <node>TYR:CE1<value>TYR:CE1</value></node>
+ <node>TYR:HE1<value>TYR:HE1</value></node>
+ <node>TYR:CZ<value>TYR:CZ</value></node>
+ <node>TYR:OH<value>TYR:OH</value></node>
+ <node>TYR:HH<value>TYR:HH</value></node>
+ <node>TYR:CE2<value>TYR:CE2</value></node>
+ <node>TYR:HE2<value>TYR:HE2</value></node>
+ <node>TYR:CD2<value>TYR:CD2</value></node>
+ <node>TYR:HD2<value>TYR:HD2</value></node>
+ <node>VAL:CA<value>VAL:CA</value></node>
+ <node>VAL:HA<value>VAL:HA</value></node>
+ <node>VAL:CB<value>VAL:CB</value></node>
+ <node>VAL:HB<value>VAL:HB</value></node>
+ <node>VAL:CG1<value>VAL:CG1</value></node>
+ <node>VAL:HG11<value>VAL:1HG1</value></node>
+ <node>VAL:HG12<value>VAL:2HG1</value></node>
+ <node>VAL:HG13<value>VAL:3HG1</value></node>
+ <node>VAL:CG2<value>VAL:CG2</value></node>
+ <node>VAL:HG21<value>VAL:1HG2</value></node>
+ <node>VAL:HG22<value>VAL:2HG2</value></node>
+ <node>VAL:HG23<value>VAL:3HG2</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.XPLOR.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,256 @@
+<node>XPLOR<value>PDB</value>
+ <node>*:H1<value>*:1H</value></node>
+ <node>*:H2<value>*:2H</value></node>
+ <node>*:H3<value>*:3H</value></node>
+ <node>*:N<value>*:N</value></node>
+ <node>*:O<value>*:O</value></node>
+ <node>*:C<value>*:C</value></node>
+ <node>*:HN<value>*:H</value></node>
+ <node>*:H<value>*:H</value></node>
+ <node>ALA:CA<value>ALA:CA</value></node>
+ <node>ALA:HA<value>ALA:HA</value></node>
+ <node>ALA:CB<value>ALA:CB</value></node>
+ <node>ALA:HB1<value>ALA:1HB</value></node>
+ <node>ALA:HB2<value>ALA:2HB</value></node>
+ <node>ALA:HB3<value>ALA:3HB</value></node>
+ <node>ARG:CA<value>ARG:CA</value></node>
+ <node>ARG:HA<value>ARG:HA</value></node>
+ <node>ARG:CB<value>ARG:CB</value></node>
+ <node>ARG:HB1<value>ARG:1HB</value></node>
+ <node>ARG:HB2<value>ARG:2HB</value></node>
+ <node>ARG:CG<value>ARG:CG</value></node>
+ <node>ARG:HG1<value>ARG:1HG</value></node>
+ <node>ARG:HG2<value>ARG:2HG</value></node>
+ <node>ARG:CD<value>ARG:CD</value></node>
+ <node>ARG:HD1<value>ARG:1HD</value></node>
+ <node>ARG:HD2<value>ARG:2HD</value></node>
+ <node>ARG:NE<value>ARG:NE</value></node>
+ <node>ARG:HE<value>ARG:HE</value></node>
+ <node>ARG:CZ<value>ARG:CZ</value></node>
+ <node>ARG:NH1<value>ARG:NH1</value></node>
+ <node>ARG:HH11<value>ARG:1HH1</value></node>
+ <node>ARG:HH12<value>ARG:2HH1</value></node>
+ <node>ARG:NH2<value>ARG:NH2</value></node>
+ <node>ARG:HH21<value>ARG:1HH2</value></node>
+ <node>ARG:HH22<value>ARG:2HH2</value></node>
+ <node>ASN:CA<value>ASN:CA</value></node>
+ <node>ASN:HA<value>ASN:HA</value></node>
+ <node>ASN:CB<value>ASN:CB</value></node>
+ <node>ASN:HB1<value>ASN:1HB</value></node>
+ <node>ASN:HB2<value>ASN:2HB</value></node>
+ <node>ASN:CG<value>ASN:CG</value></node>
+ <node>ASN:OD1<value>ASN:OD1</value></node>
+ <node>ASN:ND2<value>ASN:ND2</value></node>
+ <node>ASN:HD21<value>ASN:1HD2</value></node>
+ <node>ASN:HD22<value>ASN:2HD2</value></node>
+ <node>ASP:CA<value>ASP:CA</value></node>
+ <node>ASP:HA<value>ASP:HA</value></node>
+ <node>ASP:CB<value>ASP:CB</value></node>
+ <node>ASP:HB1<value>ASP:1HB</value></node>
+ <node>ASP:HB2<value>ASP:2HB</value></node>
+ <node>ASP:CG<value>ASP:CG</value></node>
+ <node>ASP:OD1<value>ASP:OD1</value></node>
+ <node>ASP:OD2<value>ASP:OD2</value></node>
+ <node>CYS:CA<value>CYS:CA</value></node>
+ <node>CYS:HA<value>CYS:HA</value></node>
+ <node>CYS:CB<value>CYS:CB</value></node>
+ <node>CYS:HB1<value>CYS:1HB</value></node>
+ <node>CYS:HB2<value>CYS:2HB</value></node>
+ <node>CYS:SG<value>CYS:SG</value></node>
+ <node>CYS:HG<value>CYS:HG</value></node>
+ <node>GLU:CA<value>GLU:CA</value></node>
+ <node>GLU:HA<value>GLU:HA</value></node>
+ <node>GLU:CB<value>GLU:CB</value></node>
+ <node>GLU:HB1<value>GLU:1HB</value></node>
+ <node>GLU:HB2<value>GLU:2HB</value></node>
+ <node>GLU:CG<value>GLU:CG</value></node>
+ <node>GLU:HG1<value>GLU:1HG</value></node>
+ <node>GLU:HG2<value>GLU:2HG</value></node>
+ <node>GLU:CD<value>GLU:CD</value></node>
+ <node>GLU:OE1<value>GLU:OE1</value></node>
+ <node>GLU:OE2<value>GLU:OE2</value></node>
+ <node>GLN:CA<value>GLN:CA</value></node>
+ <node>GLN:HA<value>GLN:HA</value></node>
+ <node>GLN:CB<value>GLN:CB</value></node>
+ <node>GLN:HB1<value>GLN:1HB</value></node>
+ <node>GLN:HB2<value>GLN:2HB</value></node>
+ <node>GLN:CG<value>GLN:CG</value></node>
+ <node>GLN:HG1<value>GLN:1HG</value></node>
+ <node>GLN:HG2<value>GLN:2HG</value></node>
+ <node>GLN:CD<value>GLN:CD</value></node>
+ <node>GLN:OE1<value>GLN:OE1</value></node>
+ <node>GLN:NE2<value>GLN:NE2</value></node>
+ <node>GLN:HE21<value>GLN:1HE2</value></node>
+ <node>GLN:HE22<value>GLN:2HE2</value></node>
+ <node>GLY:CA<value>GLY:CA</value></node>
+ <node>GLY:HA1<value>GLY:1HA</value></node>
+ <node>GLY:HA2<value>GLY:2HA</value></node>
+ <node>HIS:CA<value>HIS:CA</value></node>
+ <node>HIS:HA<value>HIS:HA</value></node>
+ <node>HIS:CB<value>HIS:CB</value></node>
+ <node>HIS:HB1<value>HIS:1HB</value></node>
+ <node>HIS:HB2<value>HIS:2HB</value></node>
+ <node>HIS:CG<value>HIS:CG</value></node>
+ <node>HIS:ND1<value>HIS:ND1</value></node>
+ <node>HIS:HD1<value>HIS:HD1</value></node>
+ <node>HIS:CE1<value>HIS:CE1</value></node>
+ <node>HIS:HE1<value>HIS:HE1</value></node>
+ <node>HIS:NE2<value>HIS:NE2</value></node>
+ <node>HIS:HE2<value>HIS:HE2</value></node>
+ <node>HIS:CD2<value>HIS:CD2</value></node>
+ <node>HIS:HD2<value>HIS:HD2</value></node>
+ <node>ILE:CA<value>ILE:CA</value></node>
+ <node>ILE:HA<value>ILE:HA</value></node>
+ <node>ILE:CB<value>ILE:CB</value></node>
+ <node>ILE:HB<value>ILE:HB</value></node>
+ <node>ILE:CG2<value>ILE:CG2</value></node>
+ <node>ILE:HG21<value>ILE:1HG2</value></node>
+ <node>ILE:HG22<value>ILE:2HG2</value></node>
+ <node>ILE:HG23<value>ILE:3HG2</value></node>
+ <node>ILE:CG1<value>ILE:CG1</value></node>
+ <node>ILE:HG11<value>ILE:1HG1</value></node>
+ <node>ILE:HG12<value>ILE:2HG1</value></node>
+ <node>ILE:CD1<value>ILE:CD1</value></node>
+ <node>ILE:HD11<value>ILE:1HD1</value></node>
+ <node>ILE:HD12<value>ILE:2HD1</value></node>
+ <node>ILE:HD13<value>ILE:3HD1</value></node>
+ <node>LEU:CA<value>LEU:CA</value></node>
+ <node>LEU:HA<value>LEU:HA</value></node>
+ <node>LEU:CB<value>LEU:CB</value></node>
+ <node>LEU:HB1<value>LEU:1HB</value></node>
+ <node>LEU:HB2<value>LEU:2HB</value></node>
+ <node>LEU:CG<value>LEU:CG</value></node>
+ <node>LEU:HG<value>LEU:HG</value></node>
+ <node>LEU:CD1<value>LEU:CD1</value></node>
+ <node>LEU:HD11<value>LEU:1HD1</value></node>
+ <node>LEU:HD12<value>LEU:2HD1</value></node>
+ <node>LEU:HD13<value>LEU:3HD1</value></node>
+ <node>LEU:CD2<value>LEU:CD2</value></node>
+ <node>LEU:HD21<value>LEU:1HD2</value></node>
+ <node>LEU:HD22<value>LEU:2HD2</value></node>
+ <node>LEU:HD23<value>LEU:3HD2</value></node>
+ <node>LYS:CA<value>LYS:CA</value></node>
+ <node>LYS:HA<value>LYS:HA</value></node>
+ <node>LYS:CB<value>LYS:CB</value></node>
+ <node>LYS:HB1<value>LYS:1HB</value></node>
+ <node>LYS:HB2<value>LYS:2HB</value></node>
+ <node>LYS:CG<value>LYS:CG</value></node>
+ <node>LYS:HG1<value>LYS:1HG</value></node>
+ <node>LYS:HG2<value>LYS:2HG</value></node>
+ <node>LYS:CD<value>LYS:CD</value></node>
+ <node>LYS:HD1<value>LYS:1HD</value></node>
+ <node>LYS:HD2<value>LYS:2HD</value></node>
+ <node>LYS:CE<value>LYS:CE</value></node>
+ <node>LYS:HE1<value>LYS:1HE</value></node>
+ <node>LYS:HE2<value>LYS:2HE</value></node>
+ <node>LYS:NZ<value>LYS:NZ</value></node>
+ <node>LYS:HZ1<value>LYS:1HZ</value></node>
+ <node>LYS:HZ2<value>LYS:2HZ</value></node>
+ <node>LYS:HZ3<value>LYS:3HZ</value></node>
+ <node>MET:CA<value>MET:CA</value></node>
+ <node>MET:HA<value>MET:HA</value></node>
+ <node>MET:CB<value>MET:CB</value></node>
+ <node>MET:HB1<value>MET:1HB</value></node>
+ <node>MET:HB2<value>MET:2HB</value></node>
+ <node>MET:CG<value>MET:CG</value></node>
+ <node>MET:HG1<value>MET:1HG</value></node>
+ <node>MET:HG2<value>MET:2HG</value></node>
+ <node>MET:SD<value>MET:SD</value></node>
+ <node>MET:CE<value>MET:CE</value></node>
+ <node>MET:HE1<value>MET:1HE</value></node>
+ <node>MET:HE2<value>MET:2HE</value></node>
+ <node>MET:HE3<value>MET:3HE</value></node>
+ <node>PHE:CA<value>PHE:CA</value></node>
+ <node>PHE:HA<value>PHE:HA</value></node>
+ <node>PHE:CB<value>PHE:CB</value></node>
+ <node>PHE:HB1<value>PHE:1HB</value></node>
+ <node>PHE:HB2<value>PHE:2HB</value></node>
+ <node>PHE:CG<value>PHE:CG</value></node>
+ <node>PHE:CD1<value>PHE:CD1</value></node>
+ <node>PHE:HD1<value>PHE:HD1</value></node>
+ <node>PHE:CE1<value>PHE:CE1</value></node>
+ <node>PHE:HE1<value>PHE:HE1</value></node>
+ <node>PHE:CZ<value>PHE:CZ</value></node>
+ <node>PHE:HZ<value>PHE:HZ</value></node>
+ <node>PHE:CE2<value>PHE:CE2</value></node>
+ <node>PHE:HE2<value>PHE:HE2</value></node>
+ <node>PHE:CD2<value>PHE:CD2</value></node>
+ <node>PHE:HD2<value>PHE:HD2</value></node>
+ <node>PRO:CA<value>PRO:CA</value></node>
+ <node>PRO:HA<value>PRO:HA</value></node>
+ <node>PRO:CD<value>PRO:CD</value></node>
+ <node>PRO:HD1<value>PRO:1HD</value></node>
+ <node>PRO:HD2<value>PRO:2HD</value></node>
+ <node>PRO:CG<value>PRO:CG</value></node>
+ <node>PRO:HG1<value>PRO:1HG</value></node>
+ <node>PRO:HG2<value>PRO:2HG</value></node>
+ <node>PRO:CB<value>PRO:CB</value></node>
+ <node>PRO:HB1<value>PRO:1HB</value></node>
+ <node>PRO:HB2<value>PRO:2HB</value></node>
+ <node>SER:CA<value>SER:CA</value></node>
+ <node>SER:HA<value>SER:HA</value></node>
+ <node>SER:CB<value>SER:CB</value></node>
+ <node>SER:HB1<value>SER:1HB</value></node>
+ <node>SER:HB2<value>SER:2HB</value></node>
+ <node>SER:OG<value>SER:OG</value></node>
+ <node>SER:HG<value>SER:HG</value></node>
+ <node>THR:CA<value>THR:CA</value></node>
+ <node>THR:HA<value>THR:HA</value></node>
+ <node>THR:CB<value>THR:CB</value></node>
+ <node>THR:HB<value>THR:HB</value></node>
+ <node>THR:CG2<value>THR:CG2</value></node>
+ <node>THR:HG21<value>THR:1HG2</value></node>
+ <node>THR:HG22<value>THR:2HG2</value></node>
+ <node>THR:HG23<value>THR:3HG2</value></node>
+ <node>THR:OG1<value>THR:OG1</value></node>
+ <node>THR:HG1<value>THR:HG1</value></node>
+ <node>TRP:CA<value>TRP:CA</value></node>
+ <node>TRP:HA<value>TRP:HA</value></node>
+ <node>TRP:CB<value>TRP:CB</value></node>
+ <node>TRP:HB1<value>TRP:1HB</value></node>
+ <node>TRP:HB2<value>TRP:2HB</value></node>
+ <node>TRP:CG<value>TRP:CG</value></node>
+ <node>TRP:CD1<value>TRP:CD1</value></node>
+ <node>TRP:HD1<value>TRP:HD1</value></node>
+ <node>TRP:NE1<value>TRP:NE1</value></node>
+ <node>TRP:HE1<value>TRP:HE1</value></node>
+ <node>TRP:CE2<value>TRP:CE2</value></node>
+ <node>TRP:CZ2<value>TRP:CZ2</value></node>
+ <node>TRP:HZ2<value>TRP:HZ2</value></node>
+ <node>TRP:CH2<value>TRP:CH2</value></node>
+ <node>TRP:HH2<value>TRP:HH2</value></node>
+ <node>TRP:CZ3<value>TRP:CZ3</value></node>
+ <node>TRP:HZ3<value>TRP:HZ3</value></node>
+ <node>TRP:CE3<value>TRP:CE3</value></node>
+ <node>TRP:HE3<value>TRP:HE3</value></node>
+ <node>TRP:CD2<value>TRP:CD2</value></node>
+ <node>TYR:CA<value>TYR:CA</value></node>
+ <node>TYR:HA<value>TYR:HA</value></node>
+ <node>TYR:CB<value>TYR:CB</value></node>
+ <node>TYR:HB1<value>TYR:1HB</value></node>
+ <node>TYR:HB2<value>TYR:2HB</value></node>
+ <node>TYR:CG<value>TYR:CG</value></node>
+ <node>TYR:CD1<value>TYR:CD1</value></node>
+ <node>TYR:HD1<value>TYR:HD1</value></node>
+ <node>TYR:CE1<value>TYR:CE1</value></node>
+ <node>TYR:HE1<value>TYR:HE1</value></node>
+ <node>TYR:CZ<value>TYR:CZ</value></node>
+ <node>TYR:OH<value>TYR:OH</value></node>
+ <node>TYR:HH<value>TYR:HH</value></node>
+ <node>TYR:CE2<value>TYR:CE2</value></node>
+ <node>TYR:HE2<value>TYR:HE2</value></node>
+ <node>TYR:CD2<value>TYR:CD2</value></node>
+ <node>TYR:HD2<value>TYR:HD2</value></node>
+ <node>VAL:CA<value>VAL:CA</value></node>
+ <node>VAL:HA<value>VAL:HA</value></node>
+ <node>VAL:CB<value>VAL:CB</value></node>
+ <node>VAL:HB<value>VAL:HB</value></node>
+ <node>VAL:CG1<value>VAL:CG1</value></node>
+ <node>VAL:HG11<value>VAL:1HG1</value></node>
+ <node>VAL:HG12<value>VAL:2HG1</value></node>
+ <node>VAL:HG13<value>VAL:3HG1</value></node>
+ <node>VAL:CG2<value>VAL:CG2</value></node>
+ <node>VAL:HG21<value>VAL:1HG2</value></node>
+ <node>VAL:HG22<value>VAL:2HG2</value></node>
+ <node>VAL:HG23<value>VAL:3HG2</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/PCA.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,58 @@
+<node>PCA
+  <node>Names
+		<node>Pyroglutamate</node>
+		<node>Pyroglutamat</node>
+		<node>PCA</node>
+  </node>
+  <node>Atoms
+    <node>N<value>N 0.633233 -0.738520 0.753950</value></node>
+    <node>H<value>H 0.354342 -1.687937 0.623119</value></node>
+    <node>CA<value>C -0.480480 0.254947 0.696080</value></node>
+    <node>C<value>C -1.757691 -0.270758 -0.060790</value></node>
+    <node>O<value>O -1.739275 -1.432777 -0.530185</value></node>
+    <node>CB<value>C 0.102054 1.514384 0.035819</value></node>
+    <node>CG<value>C 1.511340 1.164025 -0.440294</value></node>
+    <node>CD<value>C 1.725147 -0.277577 -0.025832</value></node>
+    <node>OE<value>O 2.716615 -0.966582 -0.238284</value></node>
+    <node>HA<value>H -0.765277 0.458788 1.753344</value></node>
+    <node>1HB<value>H -0.540287 1.847529 -0.801287</value></node>
+    <node>2HB<value>H 0.122684 2.361261 0.746090</value></node>
+    <node>1HG<value>H 1.616550 1.265144 -1.535904</value></node>
+    <node>2HG<value>H 2.282434 1.821242 0.000860</value></node>
+    <node>OXT<value>O -2.740502 0.498543 -0.143251</value></node>
+  </node>
+  <node>Bonds
+    <node>4<value>H N s</value></node>
+    <node>5<value>C CA s</value></node>
+    <node>8<value>O C d</value></node>
+    <node>11<value>CB CA s</value></node>
+    <node>13<value>CG CB s</value></node>
+    <node>17<value>CD CG s</value></node>
+    <node>19<value>CD N s</value></node>
+    <node>20<value>OE CD d</value></node>
+    <node>21<value>HA CA s</value></node>
+    <node>22<value>1HB CB s</value></node>
+    <node>23<value>2HB CB s</value></node>
+    <node>24<value>1HG CG s</value></node>
+    <node>25<value>2HG CG s</value></node>
+    <node>26<value>OXT C s</value></node>
+		<node>27<value>N CA s</value></node>
+  </node>
+	<node>Connections
+    <node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>Default
+		</node>
+		<node>PCA-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/PHE.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,103 @@
+<node>PHE
+	<node>Names
+		<node>Phenylalanine</node>
+		<node>Phenylalanin</node>
+		<node>Phe</node>
+		<node>F</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.1341407 1.351202 -0.07911759</value></node>
+		<node>3H<value>H 0.803193 2.035005 0.2534044</value></node>
+		<node>CA<value>C -0.7211604 2.001838 -1.087341</value></node>
+		<node>HA<value>H -0.07892336 2.270821 -1.926756</value></node>
+		<node>C<value>C -1.300131 3.307535 -0.5325462</value></node>
+		<node>O<value>O -0.4477309 4.171679 -0.229457</value></node>
+		<node>CB<value>C -1.791856 1.027805 -1.599674</value></node>
+		<node>1HB<value>H -1.28636 0.160502 -2.026756</value></node>
+		<node>2HB<value>H -2.380364 0.6727667 -0.7525354</value></node>
+		<node>CG<value>C -2.70873 1.607533 -2.661208</value></node>
+		<node>CD1<value>C -4.074711 1.815559 -2.387768</value></node>
+		<node>HD1<value>H -4.496757 1.527902 -1.435336</value></node>
+		<node>CD2<value>C -2.185439 1.971959 -3.916095</value></node>
+		<node>HD2<value>H -1.142983 1.801105 -4.144545</value></node>
+		<node>CE1<value>C -4.90709 2.399215 -3.358655</value></node>
+		<node>HE1<value>H -5.955226 2.557371 -3.147432</value></node>
+		<node>CE2<value>C -3.019025 2.554821 -4.88633</value></node>
+		<node>HE2<value>H -2.61471 2.832835 -5.84938</value></node>
+		<node>CZ<value>C -4.379117 2.771946 -4.606688</value></node>
+		<node>HZ<value>H -5.020426 3.217529 -5.354036</value></node>
+		<node>1H<value>H -0.4341985 1.034029 0.6931909</value></node>
+		<node>2H<value>H 0.6169096 0.5661594 -0.4922875</value></node>
+		<node>OXT<value>O -2.460581 3.26509 -0.06804343</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>24<value>CD1 CG a</value></node>
+    <node>27<value>HD1 CD1 s</value></node>
+    <node>28<value>CD2 CG a</value></node>
+    <node>31<value>HD2 CD2 s</value></node>
+    <node>32<value>CE1 CD1 a</value></node>
+    <node>35<value>HE1 CE1 s</value></node>
+    <node>36<value>CE2 CD2 a</value></node>
+    <node>39<value>HE2 CE2 s</value></node>
+    <node>40<value>CZ CE1 a</value></node>
+    <node>41<value>CZ CE2 a</value></node>
+    <node>43<value>HZ CZ s</value></node>
+    <node>44<value>1H N s</value></node>
+    <node>45<value>2H N s</value></node>
+    <node>46<value>OXT C s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>PHE-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>PHE-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>PHE-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/PRO.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,85 @@
+<node>PRO
+	<node>Names
+ 		<node>Proline</node>
+		<node>Prolin</node>
+		<node>Pro</node>
+		<node>P</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.03190848 1.374047 -0.2465853</value></node>
+		<node>CA<value>C 0.4437964 0.4522487 -1.313841</value></node>
+		<node>HA<value>H -0.4329885 0.1122399 -1.866649</value></node>
+		<node>C<value>C 1.153984 -0.7795747 -0.7384319</value></node>
+		<node>O<value>O 2.396496 -0.7261156 -0.5988901</value></node>
+		<node>CB<value>C 1.34565 1.283736 -2.23033</value></node>
+		<node>1HB<value>H 2.062533 0.6767905 -2.785621</value></node>
+		<node>2HB<value>H 0.7182986 1.840951 -2.927554</value></node>
+		<node>CG<value>C 2.02933 2.275858 -1.278275</value></node>
+		<node>1HG<value>H 3.057449 1.966999 -1.081919</value></node>
+		<node>2HG<value>H 2.018846 3.280874 -1.702292</value></node>
+		<node>CD<value>C 1.21179 2.210818 0.01815094</value></node>
+		<node>1HD<value>H 0.9135454 3.204023 0.3557259</value></node>
+		<node>2HD<value>H 1.815136 1.733186 0.791898</value></node>
+		<node>OXT<value>O 0.4228693 -1.712297 -0.3395816</value></node>
+		<node>1H<value>H -0.2823305 0.8858488 0.5799416</value></node>
+		<node>2H<value>H -0.7056003 1.96474 -0.6034356</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>CA N s</value></node>
+    <node>9<value>HA CA s</value></node>
+    <node>10<value>C CA s</value></node>
+    <node>13<value>O C d</value></node>
+    <node>14<value>CB CA s</value></node>
+    <node>18<value>1HB CB s</value></node>
+    <node>19<value>2HB CB s</value></node>
+    <node>20<value>CG CB s</value></node>
+    <node>24<value>1HG CG s</value></node>
+    <node>25<value>2HG CG s</value></node>
+    <node>26<value>CD N s</value></node>
+    <node>27<value>CD CG s</value></node>
+    <node>30<value>1HD CD s</value></node>
+    <node>31<value>2HD CD s</value></node>
+    <node>32<value>OXT C s</value></node>
+    <node>33<value>1H N s</value></node>
+    <node>34<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+ 		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+		</node>
+		<node>PRO-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+ 			</node>
+		</node>
+		<node>PRO-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+ 			</node>
+		</node>
+ 		<node>PRO-N
+ 			<node>Delete
+	 			<node>OXT</node>
+ 			</node>
+ 			<node>Properties
+ 				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Pyrrole-Skeleton.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,21 @@
+<node>Pyrrole-Skeleton
+	<node>Names
+		<node>Pyrrole-Skeleton</node>
+	</node>
+	<node>Atoms
+		<node>C1<value>C -0.028662 -0.037639 1.451927</value></node>
+		<node>N2<value>N -0.002221 -1.136686 0.619895</value></node>
+		<node>C3<value>C 0.0447 -0.76844 -0.708243</value></node>
+		<node>C4<value>C 0.046187 0.65781 -0.681334</value></node>
+		<node>C5<value>C -0.008647 1.094253 0.712146</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>C1 N2 s</value></node>
+		<node>2<value>N2 C3 d</value></node>
+		<node>3<value>C3 C4 s</value></node>
+		<node>4<value>C4 C5 d</value></node>
+		<node>5<value>C5 C1 s</value></node>
+	</node>
+	<node>Properties
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/SER.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,84 @@
+<node>SER
+	<node>Names
+		<node>Serine</node>
+		<node>Serin</node>
+		<node>Ser</node>
+		<node>S</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.1130663 1.226434 -0.1468897</value></node>
+		<node>3H<value>H 0.8968111 1.837972 0.05464922</value></node>
+		<node>CA<value>C -0.7048293 1.905604 -1.168307</value></node>
+		<node>HA<value>H -0.2017423 1.780946 -2.128185</value></node>
+		<node>C<value>C -0.7701361 3.410257 -0.8778276</value></node>
+		<node>O<value>O 0.1488766 3.858471 -0.1539113</value></node>
+		<node>CB<value>C -2.088618 1.24965 -1.250489</value></node>
+		<node>1HB<value>H -1.956628 0.1725609 -1.368818</value></node>
+		<node>2HB<value>H -2.637483 1.435655 -0.3253672</value></node>
+		<node>OG<value>O -2.817839 1.744102 -2.356831</value></node>
+		<node>HG<value>H -3.648096 1.264079 -2.429246</value></node>
+		<node>OXT<value>O -1.487331 4.10633 -1.629405</value></node>
+		<node>1H<value>H -0.4311985 1.10388 0.6950446</value></node>
+		<node>2H<value>H 0.4303224 0.3296314 -0.4862972</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>OG CB s</value></node>
+		<node>23<value>HG OG s</value></node>
+		<node>24<value>OXT C s</value></node>
+		<node>25<value>1H N s</value></node>
+		<node>26<value>2H N s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>SER-M
+			<node>Properties
+				<node>N_TERMINAL</node>
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>SER-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>SER-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/T.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,106 @@
+<node>T
+	<node>Names
+		<node>Thymine</node>
+		<node>Thymin</node>
+		<node>T</node>
+	</node>
+	<node>Atoms
+		<node>P<value>P 38.566 27.407 37.821</value></node>
+		<node>O1P<value>O 38.595 26.254 36.889</value></node>
+		<node>O2P<value>O 39.157 27.302 39.179</value></node>
+		<node>O5*<value>O 37.072 27.912 37.957</value></node>
+		<node>C5*<value>C 36.632 28.815 38.965</value></node>
+		<node>1H5*<value>H 37.233 29.724 38.959</value></node>
+		<node>2H5*<value>H 36.702 28.339 39.943</value></node>
+		<node>C4*<value>C 35.191 29.171 38.689</value></node>
+		<node>H4*<value>H 34.765 29.830 39.445</value></node>
+		<node>O4*<value>O 35.114 29.926 37.469</value></node>
+		<node>C3*<value>C 34.331 27.906 38.457</value></node>
+		<node>H3*<value>H 34.825 26.944 38.594</value></node>
+		<node>O3*<value>O 33.163 27.975 39.270</value></node>
+		<node>C2*<value>C 33.920 28.064 36.992</value></node>
+		<node>1H2*<value>H 34.360 27.260 36.402</value></node>
+		<node>2H2*<value>H 32.834 28.020 36.912</value></node>
+		<node>C1*<value>C 33.860 29.573 36.906</value></node>
+		<node>H1*<value>H 33.070 30.098 37.443</value></node>
+		<node>N1<value>N 33.730 30.096 35.526</value></node>
+		<node>C6<value>C 34.405 29.543 34.472</value></node>
+		<node>H6<value>H 35.056 28.699 34.642</value></node>
+		<node>C5<value>C 34.237 29.984 33.219</value></node>
+		<node>C5M<value>C 35.018 29.323 32.073</value></node>
+		<node>1H5M<value>H 34.762 28.265 32.021</value></node>
+		<node>2H5M<value>H 34.759 29.806 31.130</value></node>
+		<node>3H5M<value>H 36.088 29.429 32.253</value></node>
+		<node>C4<value>C 33.326 31.071 32.932</value></node>
+		<node>O4<value>O 33.094 31.529 31.816</value></node>
+		<node>N3<value>N 32.681 31.586 34.053</value></node>
+		<node>3H<value>H 31.993 32.416 33.893</value></node>
+		<node>C2<value>C 32.839 31.151 35.352</value></node>
+		<node>O2<value>O 32.225 31.690 36.276</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>P O1P s</value></node>
+		<node>2<value>P O2P d</value></node>
+		<node>3<value>P O5* s</value></node>
+		<node>4<value>O5* C5* s</value></node>
+		<node>5<value>C5* C4* s</value></node>
+		<node>6<value>C4* O4* s</value></node>
+		<node>7<value>C4* C3* s</value></node>
+		<node>8<value>C3* O3* s</value></node>
+		<node>9<value>C3* C2* s</value></node>
+		<node>10<value>C2* C1* s</value></node>
+		<node>11<value>C1* O4* s</value></node>
+		<node>12<value>C1* N1 s</value></node>
+		<node>13<value>N1 C6 s</value></node>
+		<node>14<value>C6 C5 d</value></node>
+		<node>15<value>C5 C5M s</value></node>
+		<node>16<value>C5 C4 s</value></node>
+		<node>17<value>C4 O4 d</value></node>
+		<node>18<value>C4 N3 s</value></node>
+		<node>19<value>N3 C2 s</value></node>
+		<node>20<value>C2 O2 d</value></node>
+		<node>21<value>C2 N1 s</value></node>
+		<node>22<value>C5* 1H5* s</value></node>
+		<node>23<value>C5* 2H5* s</value></node>
+		<node>24<value>C4* H4* s</value></node>
+		<node>25<value>C1* H1* s</value></node>
+		<node>26<value>C3* H3* s</value></node>
+		<node>27<value>C2* 1H2* s</value></node>
+	        <node>28<value>C2* 2H2* s</value></node>
+		<node>29<value>C6 H6 s</value></node>
+		<node>30<value>C5M 1H5M s</value></node>
+		<node>31<value>C5M 2H5M s</value></node>
+		<node>32<value>C5M 3H5M s</value></node>
+		<node>33<value>N3 3H s</value></node>
+ 	</node>
+	<node>Connections
+       		<node>5-term<value>P 3-term s 1.62 0.5</value></node>
+    		<node>3-term<value>O3* 5-term s 1.62 0.5</value></node>
+	</node>
+  	<node>Properties
+    		<node>NUCLEOTIDE</node>
+  	</node>
+  	<node>Variants
+    		<node>T-M
+      			<node>Properties
+        			<node>5_PRIME</node>
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>Default
+      			<node>Properties
+      			</node>
+    		</node>
+    		<node>T-3
+      			<node>Properties
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>T-5
+      			<node>Properties
+        			<node>5_PRIME</node>
+      			</node>
+    		</node>
+  	</node>
+</node>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/THR.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,90 @@
+<node>THR
+	<node>Names
+		<node>Threonine</node>
+		<node>Threonin</node>
+		<node>Thr</node>
+		<node>T</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.07944571 1.265783 -0.06982248</value></node>
+		<node>3H<value>H 0.9103429 1.833856 0.0462634</value></node>
+		<node>CA<value>C -0.730729 1.899472 -1.127707</value></node>
+		<node>HA<value>H -0.2399387 1.69489 -2.079941</value></node>
+		<node>C<value>C -0.7224239 3.419906 -0.9435946</value></node>
+		<node>O<value>O 0.3746189 3.909003 -0.5883108</value></node>
+		<node>CB<value>C -2.153607 1.314487 -1.182294</value></node>
+		<node>HB<value>H -2.679771 1.729994 -2.044027</value></node>
+		<node>OG1<value>O -2.862524 1.651035 -0.00717756</value></node>
+		<node>HG1<value>H -3.698466 1.178201 0.002366092</value></node>
+		<node>CG2<value>C -2.126356 -0.2100642 -1.334626</value></node>
+		<node>1HG2<value>H -3.140605 -0.5875605 -1.466431</value></node>
+		<node>2HG2<value>H -1.532317 -0.4833375 -2.207111</value></node>
+		<node>3HG2<value>H -1.690858 -0.6725402 -0.448057</value></node>
+		<node>1H<value>H -0.4419178 1.260401 0.7952214</value></node>
+		<node>2H<value>H 0.324596 0.3214647 -0.3308986</value></node>
+		<node>OXT<value>O -1.661421 4.065769 -1.458723</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>HB CB s</value></node>
+    <node>20<value>OG1 CB s</value></node>
+    <node>22<value>HG1 OG1 s</value></node>
+    <node>23<value>CG2 CB s</value></node>
+    <node>27<value>1HG2 CG2 s</value></node>
+    <node>28<value>2HG2 CG2 s</value></node>
+    <node>29<value>3HG2 CG2 s</value></node>
+    <node>30<value>1H N s</value></node>
+    <node>31<value>2H N s</value></node>
+    <node>32<value>OXT C s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>THR-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>THR-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>THR-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+			<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/TRP.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,112 @@
+<node>TRP
+	<node>Names
+		<node>Tryptophane</node>
+		<node>Tryptophan</node>
+		<node>Trp</node>
+		<node>W</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.06601259 1.26337 0.1174229</value></node>
+		<node>3H<value>H 0.6980239 1.889212 0.6011554</value></node>
+		<node>CA<value>C -0.7641827 2.069947 -0.7944807</value></node>
+		<node>HA<value>H -0.09635611 2.49911 -1.541994</value></node>
+		<node>C<value>C -1.398304 3.240995 -0.03709874</value></node>
+		<node>O<value>O -0.5874859 4.036549 0.4871631</value></node>
+		<node>CB<value>C -1.786919 1.186925 -1.524096</value></node>
+		<node>1HB<value>H -1.239827 0.4012884 -2.046958</value></node>
+		<node>2HB<value>H -2.428179 0.7027346 -0.7858279</value></node>
+		<node>CG<value>C -2.643165 1.884437 -2.539373</value></node>
+		<node>CD1<value>C -3.982776 2.050424 -2.457166</value></node>
+		<node>HD1<value>H -4.607287 1.697167 -1.648804</value></node>
+		<node>CD2<value>C -2.239992 2.518021 -3.792893</value></node>
+		<node>NE1<value>N -4.432695 2.747722 -3.558181</value></node>
+		<node>HE1<value>H -5.40488 2.982779 -3.697329</value></node>
+		<node>CE2<value>C -3.401079 3.062783 -4.417417</value></node>
+		<node>CE3<value>C -1.011219 2.68937 -4.467488</value></node>
+		<node>HE3<value>H -0.1073443 2.284464 -4.037195</value></node>
+		<node>CZ2<value>C -3.347395 3.744152 -5.642442</value></node>
+		<node>HZ2<value>H -4.246768 4.143939 -6.087246</value></node>
+		<node>CZ3<value>C -0.945238 3.371593 -5.697227</value></node>
+		<node>HZ3<value>H 0.006688994 3.489207 -6.194728</value></node>
+		<node>CH2<value>C -2.108581 3.899702 -6.284111</value></node>
+		<node>HH2<value>H -2.049103 4.422244 -7.228023</value></node>
+		<node>OXT<value>O -2.601413 3.132993 0.2872543</value></node>
+		<node>1H<value>H 0.590273 0.5789365 -0.4086703</value></node>
+		<node>2H<value>H -0.5252197 0.7968075 0.7903904</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>24<value>CD1 CG a</value></node>
+    <node>27<value>HD1 CD1 s</value></node>
+    <node>28<value>CD2 CG a</value></node>
+    <node>31<value>NE1 CD1 a</value></node>
+    <node>34<value>HE1 NE1 s</value></node>
+    <node>35<value>CE2 CD2 a</value></node>
+    <node>36<value>CE2 NE1 a</value></node>
+    <node>39<value>CE3 CD2 a</value></node>
+    <node>41<value>HE3 CE3 s</value></node>
+    <node>42<value>CZ2 CE2 a</value></node>
+    <node>45<value>HZ2 CZ2 s</value></node>
+    <node>47<value>CZ3 CE3 a</value></node>
+    <node>49<value>HZ3 CZ3 s</value></node>
+    <node>50<value>CH2 CZ2 a</value></node>
+    <node>51<value>CH2 CZ3 a</value></node>
+    <node>53<value>HH2 CH2 s</value></node>
+    <node>54<value>OXT C s</value></node>
+    <node>55<value>1H N s</value></node>
+    <node>56<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+		<node>Variants
+			<node>Default
+				<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>TRP-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>TRP-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>TRP-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/TYR.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,105 @@
+<node>TYR
+	<node>Names
+		<node>Tyrosine</node>
+		<node>Tyrosin</node>
+		<node>Tyr</node>
+		<node>Y</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.0892698 1.397582 0.01951128</value></node>
+		<node>3H<value>H 0.7468582 2.066645 0.3997705</value></node>
+		<node>CA<value>C -0.7022205 2.069859 -1.026261</value></node>
+		<node>HA<value>H -0.008099081 2.359834 -1.816127</value></node>
+		<node>C<value>C -1.325588 3.357111 -0.4775957</value></node>
+		<node>O<value>O -0.5109698 4.260831 -0.1874116</value></node>
+		<node>CB<value>C -1.734457 1.10693 -1.63201</value></node>
+		<node>1HB<value>H -1.201299 0.2395796 -2.0242</value></node>
+		<node>2HB<value>H -2.395853 0.7504926 -0.8408001</value></node>
+		<node>CG<value>C -2.557806 1.696825 -2.76258</value></node>
+		<node>CD1<value>C -3.932589 1.947373 -2.588092</value></node>
+		<node>HD1<value>H -4.418424 1.704676 -1.654011</value></node>
+		<node>CD2<value>C -1.942974 2.007092 -3.98996</value></node>
+		<node>HD2<value>H -0.8916094 1.806731 -4.138027</value></node>
+		<node>CE1<value>C -4.68326 2.520281 -3.629397</value></node>
+		<node>HE1<value>H -5.736402 2.710342 -3.483602</value></node>
+		<node>CE2<value>C -2.6951 2.579179 -5.030118</value></node>
+		<node>HE2<value>H -2.222162 2.818849 -5.971263</value></node>
+		<node>CZ<value>C -4.063968 2.83503 -4.851168</value></node>
+		<node>OH<value>O -4.785331 3.388967 -5.865766</value></node>
+		<node>HH<value>H -5.709894 3.51796 -5.645833</value></node>
+		<node>OXT<value>O -2.492483 3.282188 -0.03387626</value></node>
+		<node>1H<value>H -0.5246789 1.074702 0.7536617</value></node>
+		<node>2H<value>H 0.5865244 0.613409 -0.3778604</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>24<value>CD1 CG a</value></node>
+    <node>27<value>HD1 CD1 s</value></node>
+    <node>28<value>CD2 CG a</value></node>
+    <node>31<value>HD2 CD2 s</value></node>
+    <node>32<value>CE1 CD1 a</value></node>
+    <node>35<value>HE1 CE1 s</value></node>
+    <node>36<value>CE2 CD2 a</value></node>
+    <node>39<value>HE2 CE2 s</value></node>
+    <node>40<value>CZ CE1 a</value></node>
+    <node>41<value>CZ CE2 a</value></node>
+    <node>43<value>OH CZ s</value></node>
+    <node>45<value>HH OH s</value></node>
+    <node>46<value>OXT C s</value></node>
+    <node>47<value>1H N s</value></node>
+    <node>48<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>TYR-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>TYR-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>TYR-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/U.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,99 @@
+<node>U
+	<node>Names
+		<node>Uracil</node>
+		<node>U</node>
+	</node>
+	<node>Atoms
+		<node>P<value>P 38.566 27.407 37.821</value></node>
+		<node>O1P<value>O 38.595 26.254 36.889</value></node>
+		<node>O2P<value>O 39.157 27.302 39.179</value></node>
+		<node>O5*<value>O 37.072 27.912 37.957</value></node>
+		<node>C5*<value>C 36.632 28.815 38.965</value></node>
+		<node>1H5*<value>H 37.233 29.724 38.959</value></node>
+		<node>2H5*<value>H 36.702 28.339 39.943</value></node>
+		<node>C4*<value>C 35.191 29.171 38.689</value></node>
+		<node>H4*<value>H 34.765 29.830 39.445</value></node>
+		<node>O4*<value>O 35.114 29.926 37.469</value></node>
+		<node>C3*<value>C 34.331 27.906 38.457</value></node>
+		<node>H3*<value>H 34.825 26.944 38.594</value></node>
+		<node>O3*<value>O 33.163 27.975 39.270</value></node>
+		<node>C2*<value>C 33.920 28.064 36.992</value></node>
+		<node>1H2*<value>H 34.360 27.260 36.402</value></node>
+		<node>2H2*<value>H 32.834 28.020 36.912</value></node>
+		<node>C1*<value>C 33.860 29.573 36.906</value></node>
+		<node>H1*<value>H 33.070 30.098 37.443</value></node>
+		<node>N1<value>N 33.730 30.096 35.526</value></node>
+		<node>C6<value>C 34.405 29.543 34.472</value></node>
+		<node>H6<value>H 35.056 28.699 34.642</value></node>
+		<node>C5<value>C 34.237 29.984 33.219</value></node>
+		<node>H5<value>H 35.018 29.323 32.073</value></node>
+		<node>C4<value>C 33.326 31.071 32.932</value></node>
+		<node>O4<value>O 33.094 31.529 31.816</value></node>
+		<node>N3<value>N 32.681 31.586 34.053</value></node>
+		<node>H3<value>H 31.993 32.416 33.893</value></node>
+		<node>C2<value>C 32.839 31.151 35.352</value></node>
+		<node>O2<value>O 32.225 31.690 36.276</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>P O1P s</value></node>
+		<node>2<value>P O2P d</value></node>
+		<node>3<value>P O5* s</value></node>
+		<node>4<value>O5* C5* s</value></node>
+		<node>5<value>C5* C4* s</value></node>
+		<node>6<value>C4* O4* s</value></node>
+		<node>7<value>C4* C3* s</value></node>
+		<node>8<value>C3* O3* s</value></node>
+		<node>9<value>C3* C2* s</value></node>
+		<node>10<value>C2* C1* s</value></node>
+		<node>11<value>C1* O4* s</value></node>
+		<node>12<value>C1* N1 s</value></node>
+		<node>13<value>N1 C6 s</value></node>
+		<node>14<value>C6 C5 d</value></node>
+		<node>15<value>C5 H5 s</value></node>
+		<node>16<value>C5 C4 s</value></node>
+		<node>17<value>C4 O4 d</value></node>
+		<node>18<value>C4 N3 s</value></node>
+		<node>19<value>N3 C2 s</value></node>
+		<node>20<value>C2 O2 d</value></node>
+		<node>21<value>C2 N1 s</value></node>
+		<node>22<value>C5* 1H5* s</value></node>
+		<node>23<value>C5* 2H5* s</value></node>
+		<node>24<value>C4* H4* s</value></node>
+		<node>25<value>C1* H1* s</value></node>
+		<node>26<value>C3* H3* s</value></node>
+		<node>27<value>C2* 1H2* s</value></node>
+	        <node>28<value>C2* 2H2* s</value></node>
+		<node>29<value>C6 H6 s</value></node>
+		<node>30<value>N3 H3 s</value></node>
+ 	</node>
+	<node>Connections
+       		<node>5-term<value>P 3-term s 1.62 0.5</value></node>
+    		<node>3-term<value>O3* 5-term s 1.62 0.5</value></node>
+	</node>
+  	<node>Properties
+    		<node>NUCLEOTIDE</node>
+  	</node>
+  	<node>Variants
+    		<node>U-M
+      			<node>Properties
+        			<node>5_PRIME</node>
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>Default
+      			<node>Properties
+      			</node>
+    		</node>
+    		<node>U-3
+      			<node>Properties
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>U-5
+      			<node>Properties
+        			<node>5_PRIME</node>
+      			</node>
+    		</node>
+  	</node>
+</node>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/VAL.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,94 @@
+<node>VAL
+	<node>Names
+		<node>Valine</node>
+		<node>Valin</node>
+		<node>Val</node>
+		<node>V</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.08111785 1.2013 -0.133711</value></node>
+		<node>3H<value>H 0.9032491 1.762717 0.06032801</value></node>
+		<node>CA<value>C -0.698245 1.931722 -1.152099</value></node>
+		<node>HA<value>H -0.2125321 1.7346 -2.108571</value></node>
+		<node>C<value>C -0.5967644 3.443358 -0.9052255</value></node>
+		<node>O<value>O 0.3370198 3.799585 -0.1501447</value></node>
+		<node>CB<value>C -2.141793 1.389981 -1.219405</value></node>
+		<node>HB<value>H -2.073082 0.3006792 -1.23859</value></node>
+		<node>CG1<value>C -2.976131 1.780723 0.008393872</value></node>
+		<node>1HG1<value>H -3.953726 1.301327 -0.05053521</value></node>
+		<node>2HG1<value>H -2.483032 1.448739 0.9220271</value></node>
+		<node>3HG1<value>H -3.118463 2.860577 0.05077193</value></node>
+		<node>CG2<value>C -2.878923 1.800528 -2.501579</value></node>
+		<node>1HG2<value>H -3.809818 1.237256 -2.575363</value></node>
+		<node>2HG2<value>H -3.122159 2.862025 -2.496346</value></node>
+		<node>3HG2<value>H -2.266089 1.572718 -3.374182</value></node>
+		<node>OXT<value>O -1.142181 4.189281 -1.746952</value></node>
+		<node>1H<value>H -0.4588342 1.115157 0.7148547</value></node>
+		<node>2H<value>H 0.3376986 0.2854735 -0.4735033</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>HB CB s</value></node>
+    <node>20<value>CG1 CB s</value></node>
+    <node>24<value>1HG1 CG1 s</value></node>
+    <node>25<value>2HG1 CG1 s</value></node>
+    <node>26<value>3HG1 CG1 s</value></node>
+    <node>27<value>CG2 CB s</value></node>
+    <node>31<value>1HG2 CG2 s</value></node>
+    <node>32<value>2HG2 CG2 s</value></node>
+    <node>33<value>3HG2 CG2 s</value></node>
+    <node>34<value>OXT C s</value></node>
+    <node>35<value>1H N s</value></node>
+    <node>36<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>VAL-M
+			<node>Properties
+				<node>N_TERMINAL</node>
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>VAL-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>VAL-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ZN.db	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,18 @@
+<node>ZN
+	<node>Names
+ 		<node>Zinc ion</node>
+ 		<node>Zn2+</node>
+	</node>
+	<node>Atoms
+		<node>ZN<value>Zn 0.0 0.0 0.0</value></node>
+	</node>
+	<node>Bonds
+	</node>
+	<node>Connections
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>Default</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/functionalGroups.smarts	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,133 @@
+C[*X1](C)([*X1])[*X1]	terminal primary C(sp3)
+[C,c]([C,c])([C,c])(*)*	 total secondary C(sp3)
+[C,c]([C,c])([C,c])([C,c])*	total tertiary C(sp3)
+[C,c]([C,c])([C,c])([C,c])[C,c]	total quaternary C(sp3)
+[$([Cr,cr]([Cr,cr])([Cr,cr])(*)*),$([Cr,cr]([Cr,cr])([C,c])([*r])*)]		ring secondary C(sp3)
+[$([Cr,cr]([Cr,cr])([Cr,cr])([C,c])*),$([Cr,cr]([Cr,cr])([C,c])([C,c])[*r])]	ring tertiary C(sp3)
+[Cr,cr]([Cr,cr])([Cr,cr])([C,c])[C,c]	ring quaternary C(sp3)
+[cX3]		aromatic C(sp2)
+[Ch1,ch1]1[C,c][C,c][C,c][C,c][C,c]1	unsubstituted benzene C(sp2)
+[Ch0,ch0]1[C,c][C,c][C,c][C,c][C,c]1	substituted benzene C(sp2)
+O=CC1=CCCC=C1		non-aromatic conjugated C(sp2)
+[C,c]=[C,c](*)(*)		terminal primary C(sp2)
+C=C(C)(*)	aliphatic secondary C(sp2)
+C=C(C)(C)	aliphatic tertiary C(sp2)
+[C,c]=[C,c]=[C,c]		allenes groups
+[*X1][C,c]#C	terminal C(sp)
+**[C,c]#C	non-terminal C(sp)
+OC#N		cyanates
+O=C=N	isocyanates
+SC#N		thiocyanates
+N=C=S	isothiocyanates
+[OH,Oh]C=O	carboxylic acids
+[*;!H]OC=O	 esters
+[NH2,Nh2]C=O		primary amides
+[*;!H][NH,Nh]C=O		secondary amides
+[*;!H]N([*;!H])C=O	tertiary amides
+*N(*)C([O,S]*)=[O,S]		(thio-)carbamates
+[F,Cl,Br,I,At]C(*)=O		acyl halogenides
+[$([OH,Oh]C(*)=S),$([SH,Sh]C(*)=O)]		thioacids
+[SH,Sh]C(*)=S		dithioacids
+[$([*;!H]OC(*)=S),$([*;!H]SC(*)=O)]		thioesters
+[*;!H]SC(*)=S		dithioesters
+[CH,Ch](*)=O	aldehydes
+*C(*)=O		ketones
+[NX3]C([NX3])=[O,S]		urea (-thio) derivatives
+[OX2,SX2]C([OX2,SX2])=[O,S]	carbonate (-thio) derivatives
+[NX2]C([C,H])[NX3]	amidine derivatives
+[NX3]C(=[NX2])[NX3]	guanidine derivatives
+*C(*)=N[N,C,H]		imines
+*C(*)=NO*	oximes
+[NH2X3,Nh2X3]		primary amines
+[NH1X3,Nh1X3]		secondary amines
+[NH0X3;Nh0X3]	 tertiary amines
+[C,H][NX3][NX3][C,H]		N hydrazines
+[C,H][NX2]=[NX2][C,H]	N azo-derivatives
+N#C*	nitriles
+[N+n]	positive charged N
+[NX4]	quaternary N
+*N(*)O*	hydroxylamines
+*N(*)N=O		nitrosamine
+*N=O	nitroso groups
+*N(O)=O		nitro groups
+[CX3](=[O,S])[NX3]([H,C])[CX3]=[O,S]	imides
+[C,H]C([C,H])=NN([C,H])[C,H]	hydrazones
+A[OX2h1,OX2H1]		hydroxyl groups
+a[OX2h1,OX2H1]		aromatic hydroxyls
+C[CH2,Ch2][OH,Oh]		primary alcohols
+C[CH,Ch](C)[OH,Oh]	secondary alcohols
+CC(C)(C)[OH,Oh]	tertiary alcohols
+*O*	 ethers
+*O[F,Cl,Br,I,At]	hypohalogenides
+[CX3](=[O,S])O[CX3][O,S]	anhydrides
+[OH2,Oh2]	water
+C[SH,Sh]	thiols
+S=C(C)C	thioketones
+C[SX2]C	sulfides
+C[SX2][SX2]C	disulfides
+[$(CS(C)=O),$(C=S=O),$(S=S=O)]	sulfoxides
+[$(O=[SX4]=O),$(O=S(=[C,S])=O)]	sulfones
+[SX2][Oh1,OH1,Sh1,SH1]		sulfenic acids
+[SX3](=[O,S])[Oh1,OH1,Sh1,SH1]		sulfinic acids
+[SX4](=[O,S])(=[O,S])[Oh1,OH1,Sh1,SH1]		sulfonic acids
+[OX2,SX2][SX4](=[O,S])(=[O,S])[Oh1,OH1,Sh1,SH1]		sulfuric acids
+[SX3](=[O,S])[OX2,SX2]		sulfites
+[SX4](=[O,S])(=[O,S])[OX2,SX2]	sulfonates
+[OX2,SX2][SX4](=[O,S])(=[O,S])[OX2,SX2]	sulfates
+[$(C[SX4](=O)(=O)[NX3]),$(C[SX4](=S)(=O)[NX3]),$(C[SX3](=O)[NX3]),$(C[SX3](=S)[NX3]),$(CS[NX3])]	sulfonamides/sulfinamides/sulfenamides
+[O,S]P([O,S])[O,S]	phosphites/thiophosphites
+[O,S]P(=[O,S])([O,S])[O,S]		phosphates/thiophosphates
+[O,S]P([O,S])[O,S]	phosphanes
+[H,S,F,Cl,Br,I,At][PX4](=[S,O])([SX2,OX2])[SX2,OX2]	phosphonates/thiophosphonates
+[$([H,S,F,Cl,Br,I,At][PX4](=[S,O])([H,S,F,Cl,Br,I,At])[H,S,F,Cl,Br,I,At]),$([H,S,F,Cl,Br,I,At][PX5]([H,S,F,Cl,Br,I,At])([H,S,F,Cl,Br,I,At])([H,S,F,Cl,Br,I,At])[H,S,F,Cl,Br,I,At])]		phosphoranes/thiophosphoranes
+[F,Cl,Br,I,At][CX4h2,CX4H2,cx4h2,cx4H2][C,c]		CH2RX
+[F,Cl,Br,I,At][CX4h1,CX4H1,cX4h1,cX4H1]([C,c])[C,c]	CHR2X
+[F,Cl,Br,I,At][C,c]([C,c])([C,c])[C,c]		CR3X
+[C,c]=[CX3h1,cX3h1,CX3H1,cX3H1][F,Cl,Br,I,At]	R=CHX
+[C,c]=[C,c]([C,c])[F,Cl,Br,I,At]		R=CRX
+[F,Cl,Br,I,At]C#C		R#CX
+[F,Cl,Br,I,At][CX4h1,CX4H1,cX4h1,cX4H1]([C,c])[F,Cl,Br,I,At]	 CHRX2
+[F,Cl,Br,I,At][C,c]([C,c])([C,c])[F,Cl,Br,I,At]	CR2X2
+[C,c]=[C,c]([F,Cl,Br,I,At])[F,Cl,Br,I,At]	 R=CX2
+[F,Cl,Br,I,At][C,c]([C,c])([F,Cl,Br,I,At])[F,Cl,Br,I,At]	CRX3
+[F,Cl,Br,I,At][ar]	halogene on aromatic ring
+[CrX4,crX4][F,Cl,Br,I,At]	X on ring C(sp3)
+[CrX3,crX3][F,Cl,Br,I,At]	X on ring C(sp2)
+[C,c]=[C,c]([F,Cl,Br,I,At])[C,c]=[C,c]	 halogene on exo-conjugated C
+[N,n]1@[C,c]@[C,c]1	Aziridines
+[O,o]1@[C,c]@[C,c]1	Oxiranes
+[S,s]1@[C,c]@[C,c]1	Thiranes
+[N,n]1@[C,c]@[C,c]@[C,c]1	Azetidines
+[O,o]1@[C,c]@[C,c]@[C,c]1	Oxetanes
+[S,s]1@[C,c]@[C,c]@[C,c]1	Thioethanes
+[N,n]12@[C,c]@[C,c]@[C,c]@[C,c]@[C,c]1(@[C,c]@C2(=O))	Beta-Lactams
+[N,n]1@[C,c]@[C,c]@[C,c]1		Pyrrolidines
+[O,o]1[C,c][C,c][C,c][C,c]1	Oxolanes
+[S,s]1[C,c][C,c][C,c][C,c]1	tetrahydro-Thiophenes
+[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]1	Pyrroles
+[N,n]1@[N,n]@[C,c]@[C,c]@[C,c]1	Pyrazoles
+[N,n]1@[C,c]@[N,n]@[C,c]@[C,c]1	Imidazoles
+[O,o]1[C,c]=[C,c][C,c]=[C,c]1	Furanes
+[S,s]1[C,c]=[C,c][C,c]=[C,c]1	Thiophenes
+[O,o]1@[C,c]@[N,n]@[C,c]@[C,c]1	Oxazoles
+[O,o]1@[N,n]@[C,c]@[C,c]@[C,c]1	Isoxazoles
+[S,s]1@[C,c]@[N,n]@[C,c]@[C,c]1	Thiazoles
+[S,s]1@[N,n]@[C,c]@[C,c]@[C,c]1	Isothiazoles
+[$([N,n]1@[N,n]@[C,c]@[N,n]@C1),$([N,n]1@[N,n]@[N,n]@[C,c]@[C,c]1)]	Triazoles
+[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]@[C,c]1	Pyridines
+[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]@[N,n]1	Pyridazines
+[N,n]1@[C,c]@[C,c]@[C,c]@[N,n]@[C,c]1	Pyrimidines
+[N,n]1@[C,c]@[C,c]@[N,n]@[C,c]@[C,c]1	Pyrazines
+[N,n]1@[C,c]@[N,n]@[C,c]@[N,n]@[C,c]1	135-Triazines
+[N,n]1@[C,c]@[N,n]@[N,n]@[C,c]@[C,c]1	124-Triazines
+[C,c]1([Oh1,OH1])[C,c][C,c][C,c][C,c][C,c]1	Phenoles
+[C,c]1([C])[C,c][C,c][C,c][C,c][C,c]1	Phenyles
+[C,c]1([CH3,ch3])[C,c][C,c][C,c][C,c][C,c]1	Toluenes
+OC[C,c]1@[C,c](O)@[C,c](O)@[C,c](O)@[C,c](O)@[O,o]1	Glucose
+OC[C,c]1(O)@[C,c](O)@[C,c](O)@[C,c](CO)[O,o]1	Fructose
+[CH3,Ch3]	Methyl
+[F,Cl,Br,I,At]		Halogenides
+[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2,Ch3,CH3]	Propyl
+[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2][CH2,Ch2,Ch3,CH3]	Butyl
+[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2][CH2,Ch2][CH2,Ch2,Ch3,CH3]	Pentyl
+CC=C([CH3,Ch3])([CH3,Ch3])	Prenyl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/confFiles.py	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,32 @@
+# -*- coding: utf-8 -*-
+"""
+XML format classes
+"""
+import data
+import logging
+from galaxy.datatypes.sniff import *
+import commands
+
+log = logging.getLogger(__name__)
+
+
+class ini( data.Text ):
+	file_ext = "ini"
+	def sniff( self, filename ):
+		self.no_sections = commands.getstatusoutput("grep -c \"\[Docking-Settings\]\" "+filename)
+		if (self.no_sections[0] == 0) & (self.no_sections[1] > 0):
+			return True
+		else:
+			self.no_sections = commands.getstatusoutput("grep -c \"\[ReferenceArea\" "+filename)
+			if (self.no_sections[0] == 0) & (self.no_sections[1] > 0):
+				return True
+			else:
+				self.no_sections = commands.getstatusoutput("grep -c \"\[PharmacophoreConstraint\" "+filename)
+				if (self.no_sections[0] == 0) & (self.no_sections[1] > 0):
+					return True
+				else:
+					return False
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/countResidues.sh	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,64 @@
+#!/bin/bash
+
+IFS=$'\n';
+residue_list=""
+hetsys_list=""
+hoh_list=""
+
+for line in $(cat $1); do
+	if [ "${line:0:4}" = "ATOM"  ];then
+		residue_list+="${line:23:6}\n"
+	else
+		if [ "${line:0:6}" = "HETATM"  ];then
+			s2=`echo $line | grep HOH`
+			if [ "$s2" != "" ];then
+				hoh_list+="${line:21:8}\n"
+			else
+				s3=`echo $line | grep WAT`
+				if [ "$s3" != "" ];then
+					hoh_list+="${line:21:8}\n"
+				else
+					hetsys_list+="${line:21:8}\n"
+				fi
+			fi
+		fi
+	fi
+done
+
+IFS=$' ';
+let num_res=`echo -e "\n"$residue_list | uniq | wc -l`
+let num_hoh=`echo -e "\n"$hoh_list | uniq | wc -l`
+let num_hetsys=`echo -e "\n"$hetsys_list | uniq | wc -l`
+
+# empty line at begin and end of lists -> substract 2
+let num_res-=2
+let num_hoh-=2
+let num_hetsys-=2
+if [ $num_res -lt 0 ]; then
+	let num_res=0
+fi
+if [ $num_hoh -lt 0 ]; then
+	let num_hoh=0
+fi
+if [ $num_hetsys -lt 0 ]; then
+	let num_hetsys=0
+fi
+
+echo -n "$num_res "
+if [ $num_res -eq 1 ]; then
+	echo "residue"
+else
+	echo "residues"
+fi
+echo -n "$num_hoh water "
+if [ $num_hoh -eq 1 ]; then
+	echo "molecule"
+else
+	echo "molecules"
+fi
+echo -n "$num_hetsys "
+if [ $num_hetsys -eq 1 ]; then
+	echo "heterosystem"
+else
+	echo "heterosystems"
+fi
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/datatypes_conf.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<datatypes>
+    <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
+			<datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
+			<datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
+			<datatype extension="jpg" type="galaxy.datatypes.images:Image" mimetype="image/jpeg"/>
+			<datatype extension="gif" type="galaxy.datatypes.images:Image" mimetype="image/gif"/>
+			<datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/>
+
+			<datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
+			<datatype extension="grd.tgz" type="galaxy.datatypes.molFiles:grdtgz" display_in_upload="true"/>
+			<datatype extension="mol2" type="galaxy.datatypes.molFiles:MOL2" display_in_upload="true"/>
+			<datatype extension="sdf" type="galaxy.datatypes.molFiles:SDF" display_in_upload="true"/>
+			<datatype extension="pdb" type="galaxy.datatypes.molFiles:PDB" display_in_upload="true"/>
+			<datatype extension="drf" type="galaxy.datatypes.molFiles:DRF" display_in_upload="true"/>
+			<datatype extension="mol2/sdf/drf" type="galaxy.datatypes.molFiles:GenericMolFile" display_in_upload="true"/>
+			<datatype extension="bvp" type="galaxy.datatypes.data:Data" display_in_upload="true"/>
+			<datatype extension="ini" type="galaxy.datatypes.confFiles:ini" display_in_upload="true"/>
+
+		<!-- Datatypes for QuEasy -->
+			<datatype extension="dat" type="galaxy.datatypes.data:Text" display_in_upload="false"/>
+			<datatype extension="csv" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
+			<datatype extension="mod" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
+    </registration>
+
+    <sniffers>
+		<sniffer type="galaxy.datatypes.confFiles:ini"/>
+		<sniffer type="galaxy.datatypes.molFiles:SDF"/>
+		<sniffer type="galaxy.datatypes.molFiles:MOL2"/>
+		<sniffer type="galaxy.datatypes.molFiles:DRF"/>
+		<sniffer type="galaxy.datatypes.molFiles:PDB"/>
+    </sniffers>
+</datatypes>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/molFiles.py	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,128 @@
+# -*- coding: utf-8 -*-
+
+import data
+import logging
+from galaxy.datatypes.sniff import *
+import commands
+
+log = logging.getLogger(__name__)
+
+class GenericMolFile( data.Text ):
+	file_ext = "mol2/sdf/drf"
+	def check_filetype( self,filename ):
+		self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			self.file_ext="sdf"
+			return True
+		self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			self.file_ext="mol2"
+			return True
+		self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			self.file_ext="drf"
+			return True
+		self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			self.file_ext="pdb"
+			return True
+		return False
+
+	def set_peek( self, dataset, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			if(self.check_filetype(dataset.file_name)) :
+				if (self.no_mols[1] == '1'):
+					dataset.blurb = "1 molecule"
+				else:
+					dataset.blurb = "%s molecules"%self.no_mols[1]
+			dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+		else:
+			dataset.peek = 'file does not exist'
+			dataset.blurb = 'file purged from disk'
+
+	def get_mime(self):
+		return 'text/plain'
+
+
+class GenericMultiMolFile( GenericMolFile ):
+	def set_peek( self, dataset, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			self.sniff(dataset.file_name)
+			if (self.no_mols[1] == '1'):
+				dataset.blurb = "1 molecule"
+			else:
+				dataset.blurb = "%s molecules"%self.no_mols[1]
+			dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+		else:
+			dataset.peek = 'file does not exist'
+			dataset.blurb = 'file purged from disk'
+
+class SDF( GenericMultiMolFile ):
+	file_ext = "sdf"
+	def sniff( self, filename ):
+		self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			return True
+		else:
+			return False
+
+class MOL2( GenericMultiMolFile ):
+	file_ext = "mol2"
+	def sniff( self, filename ):
+		self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			return True
+		else:
+			return False
+
+class DRF( GenericMultiMolFile ):
+	file_ext = "drf"
+	def sniff( self, filename ):
+		self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			return True
+		else:
+			return False
+
+class PDB( GenericMolFile ):
+	file_ext = "pdb"
+	def sniff( self, filename ):
+		self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			return True
+		else:
+			return False
+	def set_peek( self, dataset, is_multi_byte=False ):
+	#def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			res = commands.getstatusoutput("lib/galaxy/datatypes/countResidues.sh "+dataset.file_name)
+			dataset.peek = res[1]
+			self.sniff(dataset.file_name)
+			if (self.no_mols[1] == '1'):
+				dataset.blurb = "1 protein structure"
+			else:
+				dataset.blurb = "%s protein structures"%self.no_mols[1]
+		else:
+			dataset.peek = 'file does not exist'
+			dataset.blurb = 'file purged from disk'
+
+class grd ( data.Text ) :
+	file_ext = "grd"
+	def set_peek( self, dataset, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			#dataset.peek = ""
+			dataset.blurb = "score-grids for docking"
+		else:
+			dataset.peek = 'file does not exist'
+			dataset.blurb = 'file purged from disk'
+
+class grdtgz ( data.Text ) :
+	file_ext = "grd.tgz"
+	def set_peek( self, dataset, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			#dataset.peek = ""
+			dataset.blurb = "compressed score-grids for docking"
+		else:
+			dataset.peek = 'file does not exist'
+			dataset.blurb = 'file purged from disk'
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tool_conf.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,71 @@
+<?xml version="1.0"?>
+<toolbox>
+  <label text="CADDSuite" id="cadds" />
+
+  <section name="Get Data" id="getext">
+    <tool file="data_source/upload.xml"/>
+    <tool file="CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml"/>
+    <tool file="CADDSuite/galaxyconfigs/tools/PDBDownload.xml"/>
+    <tool file="CADDSuite/galaxyconfigs/tools/DBExporter.xml"/>
+  </section>
+
+  <section name="Data preparation" id="dataPrep">
+	<tool file="CADDSuite/galaxyconfigs/tools/PDBCutter.xml" />
+	<tool file="CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml" />
+	<tool file="CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml" />
+	<tool file="CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml" />
+   <tool file="CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml"/>
+   <tool file="CADDSuite/galaxyconfigs/tools/EvenSplit.xml"/>
+   <tool file="CADDSuite/galaxyconfigs/tools/PropertyModifier.xml"/>
+   <tool file="CADDSuite/galaxyconfigs/tools/MolFilter.xml"/>
+  </section>
+
+  <section name="Checks and evaluations" id="checks">
+	<tool file="CADDSuite/galaxyconfigs/tools/ProteinCheck.xml" />
+	<tool file="CADDSuite/galaxyconfigs/tools/LigCheck.xml" />
+  </section>
+
+  <section name="Docking" id="dockingTools">
+	 <tool file="CADDSuite/galaxyconfigs/tools/WaterFinder.xml" />
+	 <tool file="CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml" />
+	 <tool file="CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml" />
+	 <tool file="CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml"/>
+	 <tool file="CADDSuite/galaxyconfigs/tools/PocketDetector.xml"/>
+    <tool file="CADDSuite/galaxyconfigs/tools/GridBuilder.xml" />
+    <tool file="CADDSuite/galaxyconfigs/tools/IMeedyDock.xml" />
+  </section>
+
+  <section name="Rescoring" id="rescoringsection">
+	<tool file="CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml"/>
+	<tool file="CADDSuite/galaxyconfigs/tools/TaGRes-train.xml"/>
+	<tool file="CADDSuite/galaxyconfigs/tools/TaGRes.xml"/>
+	<tool file="CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml" />
+  </section>
+
+	<section name="QuEasy (QSAR)" id="queasy">
+		<tool file="CADDSuite/galaxyconfigs/tools/InputReader.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/ModelCreator.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/FeatureSelector.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/Validator.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/MolPredictor.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/AutoModel.xml" />
+	</section>
+
+	<section name="Analysis" id="analysis">
+		<tool file="CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml"/>
+		<tool file="CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml"/>
+		<tool file="CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml"/>
+		<tool file="CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml"/>
+	</section>
+
+	<section name="Convert, combine and store" id="storeData">
+		<tool file="CADDSuite/galaxyconfigs/tools/Converter.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/MolCombine.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/DockResultMerger.xml"/>
+		<tool file="CADDSuite/galaxyconfigs/tools/Filter.xml"/>
+		<tool file="CADDSuite/galaxyconfigs/tools/MolDepict.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/DBImporter.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/VendorFinder.xml" />
+	</section>
+
+</toolbox>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,32 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.94">
+    <description>rescore w/ anti-target dock-results</description>
+    <command interpreter="bash"><![CDATA[../../AntitargetRescorer
+#if str( $t ) != ''  and str( $t ) != 'None' :
+   -t "$t"
+#end if
+#if str( $at ) != ''  and str( $at ) != 'None' :
+   -at "$at"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="t" label="input file w/ target dock-results" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="at" label="input file w/ anti-target dock-results" optional="false" type="data" format="mol2/sdf/drf"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="t"/>
+    </outputs>
+    <help>This tool rescores docking output poses.
+AntitargetRescoring can be used to try to enhance target specificity. Therefore, dock your compounds into your target of interest and into a (very) different protein and supply the docking results here. All compounds that received a very good antitarget-score will thus be penalized, i.e. they will have a much worse score within the output file.
+
+As input we need:
+    * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docket into the specified protein (i.e. the target).
+    * a file containing the same compounds docked into the antitarget.
+
+Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 'antitarget_rescore'.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/AutoModel.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,27 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="automodel" name="AutoModel" version="1.1">
+    <description>automatically find best QSAR model</description>
+    <command interpreter="bash"><![CDATA[../../AutoModel
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $min_quality ) != ''  and str( $min_quality ) != 'None' :
+   -min_quality "$min_quality"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input data-file" optional="false" type="data" format="dat"/>
+        <param name="min_quality" label="minimal desired quality (default: 0.3)" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value="0.3"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mod"/>
+    </outputs>
+    <help>This tool tries to automatically find the best QSAR model for a given data set.
+
+It therefore applies nested validation, including feature selection, for each available model-type. The model with the best nested prediction quality is saved to the specified output file. However, if the best obtained nested prediction quality is smaller than the value specified by '-min_quality', an error will be shown and no model will be saved.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,36 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.94">
+    <description>fix bindingdb.org downloads</description>
+    <command interpreter="bash"><![CDATA[../../BindingDBCleaner
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $type ) != ''  and str( $type ) != 'None' :
+   -type "$type"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $target ) != ''  and str( $target ) != 'None' :
+   -target "$target"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="type" label="type of contained activity values: 'Ki' or 'IC50'" optional="false" type="select">
+            <option value="IC50">IC50</option>
+            <option value="Ki">Ki</option>
+        </param>
+        <param name="target" label="binding-DB target name" optional="false" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool cleans up the sd-properties contained in sd-files downloaded from bindingdb.org.
+
+For all compounds in the input file, the affinity value for the specified target is searched and retained but all other properties are removed. Furthermore, the IC50 or Ki value of each compound is converted to a binding-free-energy value in units of [kJ/mol] that is added as a property-tag named 'binding_free_energy'.
+
+All compounds in the input file for which no IC50 resp. Ki value for the specified target can found, are ignored and not written to the output file.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,33 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="combilibgenerator" name="CombiLibGenerator" version="0.94">
+    <description>generate combinatorial lib</description>
+    <command interpreter="bash"><![CDATA[../../CombiLibGenerator
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input combi-lib file" optional="false" type="data" format="data"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf"/>
+    </outputs>
+    <help>This tool generates a combinatorial library by combining the given molecule scaffolds with possible combinations of moieties.
+
+As input we need a text file specifying SMARTS expressions for the desired scaffolds and R-groups. Its format should look like the following example, although you may specify as many scaffolds and as many SMARTS expressions per R-group as you need:
+
+&lt;scaffold&gt;
+      Fc1ccc(cc1)C2=C(C([R1])=NO2)c3ccnc([R2])c3
+      Fc1ccc(cc1)C2=NOC([R1])=C2cccnc([R2])c3
+&lt;moietyR1&gt;
+      [R1]C(C)(C)C
+&lt;moietyR2&gt;
+      [R2]OC(C)(C)C
+
+Output of CombiLibGenerator is a file containing created topologies. Note that this tool does *not* generate any conformations but only topologies, so that all coordinates in the output file will be zero. Thus, apply Ligand3DGenerator to the output generated by CombiLibGenerator if you need 3D conformations.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,38 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="constraintsfinder" name="ConstraintsFinder" version="0.94">
+    <description>find strongly interacting residues</description>
+    <command interpreter="bash"><![CDATA[../../ConstraintsFinder
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="ini"/>
+    </outputs>
+    <help>This tool searches protein residues with which the reference ligand interacts strongly.
+Therefore the interaction of the reference ligand to each residue is evaluated. Residues with a score worse (i.e. larger) than -2 are ignored. A maximum of 3 constraints are created for the most strongly interacting residues that met the above criterion.
+
+As input we need:
+    * a file containing a protonated protein in pdb-format
+    * a file containing a reference ligand.
+      This reference ligand should be located in the binding pocket.
+      Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+
+Output of this tool is a docking configuration file containing the created constraints. This file should in following pipeline steps be specified for grid precalculation and docking.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Converter.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,50 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="converter" name="Converter" version="0.94">
+    <description>interconvert molecular file-formats</description>
+    <command interpreter="bash"><![CDATA[../../Converter
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $f ) != ''  and str( $f ) != 'None' :
+   -f "$f"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="f" label="output format" optional="true" type="select">
+            <option value="mol2">mol2</option>
+            <option value="sdf">sdf</option>
+            <option value="drf">drf</option>
+            <option value="pdb">pdb</option>
+            <option value="ac">ac</option>
+            <option value="ent">ent</option>
+            <option value="brk">brk</option>
+            <option value="hin">hin</option>
+            <option value="mol">mol</option>
+            <option value="xyz">xyz</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf">
+            <change_format>
+                <when input="f" value="mol2" format="mol2"/>
+                <when input="f" value="sdf" format="sdf"/>
+                <when input="f" value="drf" format="drf"/>
+                <when input="f" value="pdb" format="pdb"/>
+                <when input="f" value="ac" format="ac"/>
+                <when input="f" value="ent" format="ent"/>
+                <when input="f" value="brk" format="brk"/>
+                <when input="f" value="hin" format="hin"/>
+                <when input="f" value="mol" format="mol"/>
+                <when input="f" value="xyz" format="xyz"/>
+            </change_format>
+        </data>
+    </outputs>
+    <help>This tool can be used to convert between different molecular file-formats.
+Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/DBExporter.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,97 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="dbexporter" name="DBExporter" version="0.94 (ob)">
+    <description>export molecules from data base</description>
+    <command interpreter="bash"><![CDATA[../../DBExporter
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $start_id ) != ''  and str( $start_id ) != 'None' :
+   -start_id "$start_id"
+#end if
+#if str( $end_id ) != ''  and str( $end_id ) != 'None' :
+   -end_id "$end_id"
+#end if
+#if str( $min_logP ) != ''  and str( $min_logP ) != 'None' :
+   -min_logP "$min_logP"
+#end if
+#if str( $max_logP ) != ''  and str( $max_logP ) != 'None' :
+   -max_logP "$max_logP"
+#end if
+#if str( $min_MW ) != ''  and str( $min_MW ) != 'None' :
+   -min_MW "$min_MW"
+#end if
+#if str( $max_MW ) != ''  and str( $max_MW ) != 'None' :
+   -max_MW "$max_MW"
+#end if
+#if str( $max_mols ) != ''  and str( $max_mols ) != 'None' :
+   -max_mols "$max_mols"
+#end if
+#if str( $target ) != ''  and str( $target ) != 'None' :
+   -target "$target"
+#end if
+#if str( $q ) != ''  and str( $q ) != 'None' :
+   -q "$q"
+#end if
+#if str( $min_sim ) != ''  and str( $min_sim ) != 'None' :
+   -min_sim "$min_sim"
+#end if
+#if str( $max_sim ) != ''  and str( $max_sim ) != 'None' :
+   -max_sim "$max_sim"
+#end if
+#if str( $smarts ) != ''  and str( $smarts ) != 'None' :
+   -smarts "$smarts"
+#end if
+#if str( $smarts_file ) != ''  and str( $smarts_file ) != 'None' :
+   -smarts_file "$smarts_file"
+#end if
+#if str( $uck ) != ''  and str( $uck ) != 'None' :
+   -uck "$uck"
+#end if
+#if str( $d ) != ''  and str( $d ) != 'None' :
+   -d "$d"
+#end if
+#if str( $u ) != ''  and str( $u ) != 'None' :
+   -u "$u"
+#end if
+#if str( $h ) != ''  and str( $h ) != 'None' :
+   -h "$h"
+#end if
+#if str( $port ) != ''  and str( $port ) != 'None' :
+   -port "$port"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+#if str( $s ) != ''  and str( $s ) != 'None' :
+   -s
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="mol2/sdf/drf"/>
+        <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/>
+        <param name="start_id" label="ID of the first conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="end_id" label="ID of the last conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="min_logP" label="minimal logP value" optional="true" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
+        <param name="max_logP" label="maximal logP value" optional="true" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
+        <param name="min_MW" label="minimal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="max_MW" label="maximal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="max_mols" label="max. number of molecules to be exported" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="target" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/>
+        <param name="min_sim" label="minimal average similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
+        <param name="max_sim" label="maximal similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
+        <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/>
+        <param name="uck" label="UCK key" optional="true" area="true" type="text" size="1x15"/>
+        <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/>
+        <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/>
+        <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/>
+        <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/>
+        <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/>
+        <param name="s" label="show summary of datasets in database" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf"/>
+    </outputs>
+    <help>This tool exports compounds from a database to a molecular file. Compounds can be filtered according to (among others) SMARTS expressions, logP, molecular weight, or similarity to query molecule(s) and dataset name.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/DBImporter.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,57 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="dbimporter" name="DBImporter" version="0.94 (ob)">
+    <description>import molecules into data base</description>
+    <command interpreter="bash"><![CDATA[../../DBImporter
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $target ) != ''  and str( $target ) != 'None' :
+   -target "$target"
+#end if
+#if str( $d ) != ''  and str( $d ) != 'None' :
+   -d "$d"
+#end if
+#if str( $u ) != ''  and str( $u ) != 'None' :
+   -u "$u"
+#end if
+#if str( $h ) != ''  and str( $h ) != 'None' :
+   -h "$h"
+#end if
+#if str( $port ) != ''  and str( $port ) != 'None' :
+   -port "$port"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+#if str( $vn ) != ''  and str( $vn ) != 'None' :
+   -vn "$vn"
+#end if
+#if str( $vid ) != ''  and str( $vid ) != 'None' :
+   -vid "$vid"
+#end if
+#if str( $vd ) != ''  and str( $vd ) != 'None' :
+   -vd "$vd"
+#end if
+#if str( $vu ) != ''  and str( $vu ) != 'None' :
+   -vu "$vu"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="target" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/>
+        <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/>
+        <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/>
+        <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/>
+        <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/>
+        <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/>
+        <param name="vn" label="name of compound vendor" optional="true" area="true" type="text" size="1x15"/>
+        <param name="vid" label="name of vendor's compound-ID tag in sd-file" optional="true" area="true" type="text" size="1x15"/>
+        <param name="vd" label="vendor library date or version" optional="true" area="true" type="text" size="1x15"/>
+        <param name="vu" label="url from wich vendor library was obtained" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs/>
+    <help>This tool imports molecules into a database.
+As input we need the file containing the molecules to be imported in sd-, mol2- or drf-format.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,49 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="dockresultmerger" name="DockResultMerger" version="0.94">
+    <description>merge docking output files</description>
+    <command interpreter="bash"><![CDATA[../../DockResultMerger
+#for $s in $series_i
+   #if str( "${s.i.file_name}" ) != ''  and str( "${s.i.file_name}" ) != 'None' :
+      -i "${s.i.file_name}"
+   #end if
+#end for
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $score ) != ''  and str( $score ) != 'None' :
+   -score "$score"
+#end if
+#if str( $min ) != ''  and str( $min ) != 'None' :
+   -min "$min"
+#end if
+#if str( $max ) != ''  and str( $max ) != 'None' :
+   -max "$max"
+#end if
+#if str( $k ) != ''  and str( $k ) != 'None' :
+   -k "$k"
+#end if
+#if str( $rm ) != ''  and str( $rm ) != 'None' :
+   -rm
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <repeat name="series_i" title="input files" min="1">
+            <param name="i" label="input files" optional="false" type="data" format="mol2/sdf/drf"/>
+        </repeat>
+        <param name="score" label="score property name" optional="true" area="true" type="text" size="1x15" value="score"/>
+        <param name="min" label="minimal score value" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="max" label="maximal score value" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="k" label="number of output molecules" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="rm" label="remove input files after merging" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool merges and sorts molecule files as generated by docking or rescoring.
+
+You need to specify the property-tag name of the scores according to which the molecules should be sorted. Optionally you can filter those compounds that were assigned a score above and/or below specified thresholds. If desired, you can furthermore choose to have only the compounds with the k best scores written to the output file.
+
+ Output of DockResultMerger is one molecule containing the molecules found in input-files (that matched all filter criteria, if any), sorted ascendingly according to their scores.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/EvenSplit.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,41 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="evensplit" name="EvenSplit" version="0.94">
+    <description>generate splits w/ equal property range</description>
+    <command interpreter="bash"><![CDATA[../../EvenSplit
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o1 ) != ''  and str( $o1 ) != 'None' :
+   -o1 "$o1"
+#end if
+#if str( $o2 ) != ''  and str( $o2 ) != 'None' :
+   -o2 "$o2"
+#end if
+#if str( $n ) != ''  and str( $n ) != 'None' :
+   -n "$n"
+#end if
+#if str( $offset ) != ''  and str( $offset ) != 'None' :
+   -offset "$offset"
+#end if
+#if str( $k ) != ''  and str( $k ) != 'None' :
+   -k "$k"
+#end if
+#if str( $prop ) != ''  and str( $prop ) != 'None' :
+   -prop "$prop"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="n" label="number of compounds to use from input file" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="offset" label="extract each (i+offset)%k == 0 for o2" optional="true" type="text" area="true" size="1x5" value="0"/>
+        <param name="k" label="extract each k'th compound for 2nd output file" optional="true" type="text" area="true" size="1x5" value="2"/>
+        <param name="prop" label="property name" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
+    </inputs>
+    <outputs>
+        <data name="o1" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o2" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool splits a molecule file into two subsets in such a way that each of them convers an equal range of a property. The property with respect to which this is to be done should be specified with '-prop'.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/FeatureSelector.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,41 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="featureselector" name="FeatureSelector" version="1.1">
+    <description>run feature-selection on a QSAR model</description>
+    <command interpreter="bash"><![CDATA[../../FeatureSelector
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $dat ) != ''  and str( $dat ) != 'None' :
+   -dat "$dat"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $type ) != ''  and str( $type ) != 'None' :
+   -type "$type"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input mod-file" optional="false" type="data" format="mod"/>
+        <param name="dat" label="data-file" optional="false" type="data" format="dat"/>
+        <param name="type" label="feature-selection type" optional="false" type="select">
+            <option value="remove_correlated">remove_correlated</option>
+            <option value="forward_selection">forward_selection</option>
+            <option value="backward_selection">backward_selection</option>
+            <option value="stepwise_selection">stepwise_selection</option>
+            <option value="twinscan">twinscan</option>
+            <option value="removeLowResponseCorrelation">removeLowResponseCorrelation</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="o" format="mod"/>
+    </outputs>
+    <help>FeatureSelector runs a feature-selection for a given QSAR model.
+
+The type of feature-selection to be done is specified by '-type'. Input of this tool is a data file as generated by InputReader containing the training data for feature-selection and a QSAR model file as generated by ModelCreator (or this tool itself). Note that you can apply several feature-selection methods in succession by using the output of one call of this tool as input for the next call.
+Model- and kernel-parameters (if any) will be automatically optimized by cross-validation after applying the desired feature-selection.
+
+Output of this tool is a model-file that can be used by other QuEasy tools (e.g. Validator).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,30 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.94">
+    <description>generate galaxy tool-config files</description>
+    <command interpreter="bash"><![CDATA[../../GalaxyConfigGenerator
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ignore ) != ''  and str( $ignore ) != 'None' :
+   -ignore "$ignore"
+#end if
+#if str( $s ) != ''  and str( $s ) != 'None' :
+   -s "$s"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input par-file" optional="false" type="data" format="data"/>
+        <param name="ignore" label="tool-parameter to be ignored, i.e. those for which no galaxy config entry should be created" optional="true" area="true" size="1x5"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="xml"/>
+        <data name="s" format="data"/>
+    </outputs>
+    <help>This tool can be used to create galaxy tool-configuration files.
+As input, please supply a parameter-file as written by '-write_par' by all of our tools.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/GridBuilder.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,38 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="gridbuilder" name="GridBuilder" version="0.94">
+    <description>create score-grids for docking</description>
+    <command interpreter="bash"><![CDATA[../../GridBuilder
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $grd ) != ''  and str( $grd ) != 'None' :
+   -grd "$grd"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+    </inputs>
+    <outputs>
+        <data name="grd" format="grd.tgz"/>
+    </outputs>
+    <help>This tool precalculates a score-grid for a binding pocket of a given receptor.
+
+As input we need:
+    * a file containing a protonated protein in pdb-format
+    * a file containing a reference ligand.
+      This reference ligand should be located in the binding pocket,
+      so that a grid can be precalculated around it.
+      Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+
+Output of this tool is a file containing the score-grids that can be used by docking-/scoring-tools (e.g. IMeedyDock).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/IMGDock.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,47 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="imeedydock" name="IMGDock" version="0.94">
+    <description>Iterative Multi-Greedy Docking</description>
+    <command interpreter="bash"><![CDATA[../../IMGDock
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $grd ) != ''  and str( $grd ) != 'None' :
+   -grd "$grd"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+        <param name="i" label="compounds to be docked" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="grd" label="ScoreGrid file" optional="false" type="data" format="grd.tgz"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>IMGDock docks compounds into the binding pocket of a receptor using an iterative multi-greedy approach.
+As input we need:
+
+    * a file containing a protonated protein in pdb-format
+    * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+    * a score-grid file generated by GridBuilder. This grid must have been precalculated for the same receptor and reference ligand as those that are to be used here.
+    * a file containing the compounds that are to be docked. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). These molecules must have been assigned 3D coordinates (e.g. by Ligand3DGenerator) and should have been checked for errors using LigCheck.
+
+Output of this tool is a file containing all compounds docked into the binding pocket, with a property-tag named 'score' indicating the score obtained for each compound.
+
+Tip: If you want to parallelize docking, use LigandFileSplitter to separate your input file containing the compounds to be docked into several batches, dock each batch with this tool and merge the output files with DockResultMerger.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/InputPartitioner.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,28 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="inputpartitioner" name="InputPartitioner" version="1.1">
+    <description>split QSAR data set</description>
+    <command interpreter="bash"><![CDATA[../../InputPartitioner
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $n ) != ''  and str( $n ) != 'None' :
+   -n "$n"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input data-file" optional="false" type="data" format="dat"/>
+        <param name="n" label="number of partitions" optional="false" type="text" area="true" size="1x5" value=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="dat"/>
+    </outputs>
+    <help>InputPartitioner partitions a given QSAR data set into n partitions with evenly distributed response values.
+Thus, this tool can be useful as part of a nested validation pipeline.
+Input is a data file as generated by InputReader.
+Output will be written to n files postfixed '_TRAIN&lt;i&gt;.dat' and '_TEST&lt;i&gt;.dat', where &lt;i&gt; is the ID of the resp. partition. For each of these partitions, the training set contains only those compounds that were not selected for the resp. test set.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/InputReader.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,68 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="inputreader" name="InputReader" version="1.1">
+    <description>generate QSAR data set</description>
+    <command interpreter="bash"><![CDATA[../../InputReader
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $act ) != ''  and str( $act ) != 'None' :
+   -act "$act"
+#end if
+#if str( $csv ) != ''  and str( $csv ) != 'None' :
+   -csv "$csv"
+#end if
+#if str( $csv_nr ) != ''  and str( $csv_nr ) != 'None' :
+   -csv_nr "$csv_nr"
+#end if
+#if str( $csv_sep ) != ''  and str( $csv_sep ) != 'None' :
+   -csv_sep "$csv_sep"
+#end if
+#if str( $sdp ) != ''  and str( $sdp ) != 'None' :
+   -sdp
+#end if
+#if str( $no_cd ) != ''  and str( $no_cd ) != 'None' :
+   -no_cd
+#end if
+#if str( $no_cr ) != ''  and str( $no_cr ) != 'None' :
+   -no_cr
+#end if
+#if str( $csv_cl ) != ''  and str( $csv_cl ) != 'None' :
+   -csv_cl
+#end if
+#if str( $csv_dl ) != ''  and str( $csv_dl ) != 'None' :
+   -csv_dl
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input sd-file" optional="false" type="data" format="sdf"/>
+        <param name="csv" label="input csv-file w/ additional descriptors" optional="true" type="data" format="csv"/>
+        <param name="act" label="sd-property containing response values" optional="true" area="true" type="text" size="1x15"/>
+        <param name="csv_nr" label="no. of response variables in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="csv_sep" label="separator symbol in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="sdp" label="use sd-properties as additional descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="no_cd" label="do not center descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="no_cr" label="do not center response values" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="csv_cl" label="csv-file has compound (row) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="csv_dl" label="csv-file has descriptor (column) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="dat"/>
+    </outputs>
+    <help>This tool reads input from sd-files and generate features for QSAR analysis.
+Activity data (response values) for a training set are taken from sd-properties of the input file; the name of this property can be specified by option '-act'.
+The following number of features will be automatically created for each molecule in your sd-file:
+
+    * 40 atom and bond count descriptors
+    * 2 connectivity indices (Balaban and Zagreb index)
+    * 4 partial charge descriptors
+    * 14 surface descriptors
+    * 133 topological descriptors (functional group counts)
+
+If desired, you can also read additional descriptors from a csv-file; in this case you need to specify the file with the above options.
+Output of this tool is a data file that can be used by other QuEasy tools (e.g. ModelCreator).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,37 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.94">
+    <description>define interaction constraint</description>
+    <command interpreter="bash"><![CDATA[../../InteractionConstraintDefiner
+#if str( $res ) != ''  and str( $res ) != 'None' :
+   -res "$res"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $s ) != ''  and str( $s ) != 'None' :
+   -s "$s"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="ini" label="input configuration file" optional="true" type="data" format="ini"/>
+        <param name="res" label="residue ID" optional="false" area="true" type="text" size="1x15"/>
+        <param name="s" label="desired minimal interation (score) between ligand and specified residue(s)" optional="false" type="text" area="true" size="1x5" value="-2.0"/>
+        <param name="p" label="penalty value" optional="false" type="text" area="true" size="1x5" value="10"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="ini"/>
+    </outputs>
+    <help>This tool allows to define interaction constraints for docking or scoring.
+
+The constraint to be created will enforce a specified minimal interaction between ligands and the specified residue(s) of the receptor. Please specify residue IDs in the following manner: &lt;chain-ID&gt;:&lt;residue-ID&gt;, e.g. A:57. If you want to use more than one residue, separate their IDs by commas, e.g. A:57,B:17.
+
+Output of this tool is a ini-file that contains the desired interaction constraint.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/LigCheck.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,45 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="ligcheck" name="LigCheck" version="0.94">
+    <description>check molecules for errors</description>
+    <command interpreter="bash"><![CDATA[../../LigCheck
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ef ) != ''  and str( $ef ) != 'None' :
+   -ef "$ef"
+#end if
+#if str( $ri ) != ''  and str( $ri ) != 'None' :
+   -ri
+#end if
+#if str( $ut ) != ''  and str( $ut ) != 'None' :
+   -ut
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ef" label="error fraction; print error if fraction of invalid mols is larger" optional="true" type="text" area="true" size="1x5" value="0.5"/>
+        <param name="ri" label="remove invalid molecules." optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="ut" label="check for unique topologies (default: check only for unique conformation)" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+
+The following checks are done for each molecule:
+
+    * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
+    * each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments.
+    * each atom must have a valid assigned element
+    * the molecule must be protonated (since this is necessary for docking/(re-)scoring).
+    * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
+    * partial charges may not contain completely senseless values (&gt;5 or &lt;-5).
+    * each conformation should appear only once within the given file, otherwise it is rejected and not written to the output file. However, if option '-ut' is used, molecules will instead be checked for unique topologies.
+
+If option '-ri' is used, only those molecules that pass all those tests are written to the output file. If this option is not used, all molecules are written to output containing a property 'score_ligcheck' with a value of 1 if the molecule passed all tests or with a value of 0 if it did not pass them.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,30 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.94">
+    <description>generate 3D coordinates for small molecules</description>
+    <command interpreter="bash"><![CDATA[../../Ligand3DGenerator
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ph ) != ''  and str( $ph ) != 'None' :
+   -ph "$ph"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ph" label="pH-value for pH-dep. protonation" optional="true" type="text" area="true" size="1x5" value="7.0"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool generates 3D conformations for small molecules and adds hydrogens to them.
+As input we only a chemical file containing valid topologies. Any 2D or 3D conformations in the input file are ignored, but the existence of the correct bond-orders is necessary.
+
+Note however, that the main purpose of this tool is to generate feasible start-conformations for docking or other optimization procedures. Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules) different fragments might still overlap with each other.
+
+Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,84 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.94">
+    <description>split molecule files</description>
+    <command interpreter="bash"><![CDATA[../../LigandFileSplitter
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $no ) != ''  and str( $no ) != 'None' :
+   -no "$no"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $o2 ) != ''  and str( $o2 ) != 'None' :
+   -o "$o2"
+#end if
+#if str( $o3 ) != ''  and str( $o3 ) != 'None' :
+   -o "$o3"
+#end if
+#if str( $o4 ) != ''  and str( $o4 ) != 'None' :
+   -o "$o4"
+#end if
+#if str( $o5 ) != ''  and str( $o5 ) != 'None' :
+   -o "$o5"
+#end if
+#if str( $o6 ) != ''  and str( $o6 ) != 'None' :
+   -o "$o6"
+#end if
+#if str( $o7 ) != ''  and str( $o7 ) != 'None' :
+   -o "$o7"
+#end if
+#if str( $o8 ) != ''  and str( $o8 ) != 'None' :
+   -o "$o8"
+#end if
+#if str( $o9 ) != ''  and str( $o9 ) != 'None' :
+   -o "$o9"
+#end if
+#if str( $o10 ) != ''  and str( $o10 ) != 'None' :
+   -o "$o10"
+#end if
+#if str( $o11 ) != ''  and str( $o11 ) != 'None' :
+   -o "$o11"
+#end if
+#if str( $o12 ) != ''  and str( $o12 ) != 'None' :
+   -o "$o12"
+#end if
+#if str( $o13 ) != ''  and str( $o13 ) != 'None' :
+   -o "$o13"
+#end if
+#if str( $o14 ) != ''  and str( $o14 ) != 'None' :
+   -o "$o14"
+#end if
+#if str( $o15 ) != ''  and str( $o15 ) != 'None' :
+   -o "$o15"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="no" label="no. of splits to be created" optional="false" type="hidden" area="true" size="1x5" value="15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o2" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o3" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o4" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o5" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o6" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o7" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o8" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o9" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o10" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o11" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o12" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o13" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o14" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o15" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>LigandFileSplitter splits a molecule file into a given number of subsets.
+Note that the molecules are not sorted in any way for this.
+
+Since Galaxy does not support a flexible number of output-files, we will create 15 output files when you use LigandFileSplitter in Galaxy.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ModelCreator.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,52 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="modelcreator" name="ModelCreator" version="1.1">
+    <description>create a QSAR model</description>
+    <command interpreter="bash"><![CDATA[../../ModelCreator
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $type ) != ''  and str( $type ) != 'None' :
+   -type "$type"
+#end if
+#if str( $kernel ) != ''  and str( $kernel ) != 'None' :
+   -kernel "$kernel"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input dat-file" optional="false" type="data" format="dat"/>
+        <param name="type" label="model type" optional="false" type="select">
+            <option value="MLR">MLR</option>
+            <option value="RR">RR</option>
+            <option value="PCR">PCR</option>
+            <option value="PLS">PLS</option>
+            <option value="OPLS">OPLS</option>
+            <option value="ALL">ALL</option>
+            <option value="KNN">KNN</option>
+            <option value="KPLS">KPLS</option>
+            <option value="KPCR">KPCR</option>
+            <option value="GP">GP</option>
+            <option value="LDA">LDA</option>
+            <option value="snB">snB</option>
+            <option value="nB">nB</option>
+        </param>
+        <param name="kernel" label="kernel type (in case of kernel-model)" optional="true" type="select">
+            <option value="none">none</option>
+            <option value="polynomial">polynomial</option>
+            <option value="rbf">rbf</option>
+            <option value="sigmoidal">sigmoidal</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="o" format="mod"/>
+    </outputs>
+    <help>ModelCreator creates a QSAR model using an input data set as generated by InputReader.
+
+The type of QSAR model to be used can be specified by '-type', the type of kernel-function (if any) can be chosen by '-kernel'. Optimization of model- and kernel-parmeters will be done automatically using cross-validation.
+
+Output of this tool is a model-file that can be used by other QuEasy tools (e.g. FeatureSelector).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolCombine.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,45 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="molcombine" name="MolCombine" version="0.94">
+    <description>combine molecular files</description>
+    <command interpreter="bash"><![CDATA[../../MolCombine
+#if str( $i1 ) != ''  and str( $i1 ) != 'None' :
+   -i1 "$i1"
+#end if
+#if str( $i2 ) != ''  and str( $i2 ) != 'None' :
+   -i2 "$i2"
+#end if
+#if str( $mode ) != ''  and str( $mode ) != 'None' :
+   -mode "$mode"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ignH ) != ''  and str( $ignH ) != 'None' :
+   -ignH
+#end if
+#if str( $replace_prop ) != ''  and str( $replace_prop ) != 'None' :
+   -replace_prop
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i1" label="input molecule file A" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="i2" label="input molecule file B" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="mode" label="'intersection', 'union' or 'b_not_a'" optional="false" type="select">
+            <option value="intersection">intersection</option>
+            <option value="union">union</option>
+            <option value="b_not_a">b_not_a</option>
+        </param>
+        <param name="ignH" label="ignore hydrogens, i.e. match molecules to any protonation state." optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="replace_prop" label="replace properties from file 1 w/ those from file 2" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i1"/>
+    </outputs>
+    <help>This tool generates the intersection or union of two given chemical files. Property-tags of molecules that appear in both input files are automatically merged.
+
+If you want to match molecules regardless of their protonation state, use option '-ignH'.
+
+Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolDepict.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,28 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="moldepict" name="MolDepict" version="0.94">
+    <description>create structure diagrams</description>
+    <command interpreter="bash"><![CDATA[../../MolDepict
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $max ) != ''  and str( $max ) != 'None' :
+   -max "$max"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="max" label="maximal number of pictures (default=60, 0=unlimited)" optional="true" type="text" area="true" size="1x5" value="60"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="pdf"/>
+    </outputs>
+    <help>This tool create structure diagrams for small molecules.
+Supported input-formats are mol, mol2, sdf, drf.
+
+Output of this tool is one pdf-file containing the structure diagrams for all molecules in the input-file.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolFilter.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,60 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="molfilter" name="MolFilter" version="0.9">
+    <description>filter molecule files</description>
+    <command interpreter="bash"><![CDATA[../../MolFilter
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $min_logP ) != ''  and str( $min_logP ) != 'None' :
+   -min_logP "$min_logP"
+#end if
+#if str( $max_logP ) != ''  and str( $max_logP ) != 'None' :
+   -max_logP "$max_logP"
+#end if
+#if str( $min_MW ) != ''  and str( $min_MW ) != 'None' :
+   -min_MW "$min_MW"
+#end if
+#if str( $max_MW ) != ''  and str( $max_MW ) != 'None' :
+   -max_MW "$max_MW"
+#end if
+#if str( $q ) != ''  and str( $q ) != 'None' :
+   -q "$q"
+#end if
+#if str( $min_sim ) != ''  and str( $min_sim ) != 'None' :
+   -min_sim "$min_sim"
+#end if
+#if str( $max_sim ) != ''  and str( $max_sim ) != 'None' :
+   -max_sim "$max_sim"
+#end if
+#if str( $smarts ) != ''  and str( $smarts ) != 'None' :
+   -smarts "$smarts"
+#end if
+#if str( $smarts_file ) != ''  and str( $smarts_file ) != 'None' :
+   -smarts_file "$smarts_file"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+-quiet
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input molecule-file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="txt"/>
+        <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/>
+        <param name="min_logP" label="minimal logP value" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="max_logP" label="maximal logP value" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="min_MW" label="minimal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="max_MW" label="maximal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="min_sim" label="minimal average similarity" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="max_sim" label="maximal similarity" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>MolFilter can filter molecules from a molecule input file according to SMARTS expressions, logP, molecular weight, or similarity to query molecule(s).
+
+Output of this tool is a molecule file that contains all compounds that fulfilled the specified search criteria.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolPredictor.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,50 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="molpredictor" name="MolPredictor" version="1.1">
+    <description>predict molecule activities with QSAR model</description>
+    <command interpreter="bash"><![CDATA[../../MolPredictor
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $mod ) != ''  and str( $mod ) != 'None' :
+   -mod "$mod"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $csv ) != ''  and str( $csv ) != 'None' :
+   -csv "$csv"
+#end if
+#if str( $csv_nr ) != ''  and str( $csv_nr ) != 'None' :
+   -csv_nr "$csv_nr"
+#end if
+#if str( $csv_sep ) != ''  and str( $csv_sep ) != 'None' :
+   -csv_sep "$csv_sep"
+#end if
+#if str( $csv_cl ) != ''  and str( $csv_cl ) != 'None' :
+   -csv_cl
+#end if
+#if str( $csv_dl ) != ''  and str( $csv_dl ) != 'None' :
+   -csv_dl
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input sd-file" optional="false" type="data" format="sdf"/>
+        <param name="mod" label="file containing QSAR model" optional="false" type="data" format="mod"/>
+        <param name="csv" label="input csv-file w/ additional descriptors" optional="true" type="data" format="csv"/>
+        <param name="csv_nr" label="no. of response variables in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="csv_sep" label="separator symbol in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="csv_cl" label="csv-file has compound (row) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="csv_dl" label="csv-file has descriptor (column) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="sdf"/>
+    </outputs>
+    <help>This tool predictes the response values of compounds in the given molecule file using the specified QSAR model.
+
+Input of this tool is a molecule file (sdf,mol2,drf) and a model-file as generated by ModelCreator or FeatureSelector.
+Features for all molecules in the input file are generated automatically. However, if you used an additional, externally generated feature-set to generate your QSAR model, make sure to generate features in the same manner (i.e. using the same external tool with the same settings) for the molecule file to be used here and specify the csv-file with the above options.
+
+Output of this tool (as specified by '-o') is a molecule file containing the predicted values as a property tag named 'predicted_activity'.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PDBCutter.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,46 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="pdbcutter" name="PDBCutter" version="0.94">
+    <description>separate ligand and receptor</description>
+    <command interpreter="bash"><![CDATA[../../PDBCutter
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $lig ) != ''  and str( $lig ) != 'None' :
+   -lig "$lig"
+#end if
+#if str( $lig_chain ) != ''  and str( $lig_chain ) != 'None' :
+   -lig_chain "$lig_chain"
+#end if
+#if str( $lig_name ) != ''  and str( $lig_name ) != 'None' :
+   -lig_name "$lig_name"
+#end if
+#if str( $rm_ch ) != ''  and str( $rm_ch ) != 'None' :
+   -rm_ch "$rm_ch"
+#end if
+#if str( $rm_res ) != ''  and str( $rm_res ) != 'None' :
+   -rm_res "$rm_res"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="lig_chain" label="chain-name of ligand" optional="false" area="true" type="text" size="1x15"/>
+        <param name="lig_name" label="ligand name" optional="false" area="true" type="text" size="1x15"/>
+        <param name="rm_ch" label="protein chains that are to be deleted" optional="true" area="true" type="text" size="1x15"/>
+        <param name="rm_res" label="pdb-residues that are to be deleted (e.g. water or ions)" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="rec" format="pdb"/>
+        <data name="lig" format="pdb"/>
+    </outputs>
+    <help>This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively.
+
+The name of the reference ligand (exactly as it appears in the pdb-file) and the name of its chain need to be specified by '-lig_name' and '-lig_chain'.
+Optionally, chains (e.g. in case of multimers) or pdb-residues (e.g. water or ions) that you don't need can be deleted from the receptor. In this case, specify their names with '-rm_ch' or '-rm_res'.
+
+Output of this tool is one pdb-file containing the receptor-structure, i.e. the protein w/o reference ligand and w/o undesired chains/residues (if any were specified), and one pdb-file containing the reference ligand.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PDBDownload.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,25 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="pdbdownload" name="PDBDownload" version="0.94">
+    <description>retrieve pdb-file from pdb.org</description>
+    <command interpreter="bash"><![CDATA[../../PDBDownload
+#if str( $id ) != ''  and str( $id ) != 'None' :
+   -id "$id"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="id" label="PDB ID for desired structure" optional="false" area="true" type="text" size="1x15"/>
+        <param name="p" label="proxy" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="pdb"/>
+    </outputs>
+    <help>Download a pdb-file from the pdb data bank (http://www.pdb.org/) using the specified ID of the desired protein structure.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,26 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="partialchargescopy" name="PartialChargesCopy" version="0.94">
+    <description>transfer part. charges between files</description>
+    <command interpreter="bash"><![CDATA[../../PartialChargesCopy
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $chr ) != ''  and str( $chr ) != 'None' :
+   -chr "$chr"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="chr" label="file containing the same molecules as the input file, but with (different) partial charges" optional="false" type="data" format="mol2"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2" format_source="i"/>
+    </outputs>
+    <help>This tool copies partial charges from a given file to the conformations read from a different file.
+This can be useful when computing partial charges with external tools, most of which write output as mol2-files *without* support for storing molecular properties. By use of this tool we can thus assign the computed partial charges to the original molecules, thus retaining all properties.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PocketDetector.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,38 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="pocketdetector" name="PocketDetector" version="0.94">
+    <description>detect binding pocket</description>
+    <command interpreter="bash"><![CDATA[../../PocketDetector
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="input ini file" optional="true" type="data" format="ini"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="ini"/>
+    </outputs>
+    <help>This tool tries to detect the binding pocket in which the reference ligand is located.
+Therefore, probe atoms are placed above the protein surface at positions of relative deep burial. The cluster of probe atoms around the geometric center of the reference ligand is used for the description of the binding pocket.
+
+As input we need:
+    * a file containing a protonated protein in pdb-format. Furthermore, it should contain only relevant (i.e. strongly bound) water molecules as detected by WaterFinder.
+    * a file containing a reference ligand.
+      This reference ligand should be located in the binding pocket.
+      Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+
+Output of this tool is a docking configuration file that contains the description of the detected binding pocket. This file should in following pipeline steps be specified for docking and rescoring.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Predictor.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,30 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="predictor" name="Predictor" version="1.1">
+    <description>predict activities with QSAR model</description>
+    <command interpreter="bash"><![CDATA[../../Predictor
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $dat ) != ''  and str( $dat ) != 'None' :
+   -dat "$dat"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input mod-file" optional="false" type="data" format="mod"/>
+        <param name="dat" label="data-file containing prediction data set" optional="false" type="data" format="dat"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="txt"/>
+    </outputs>
+    <help>This tool predictes the response values of compounds in the given data-file using the specified QSAR model.
+
+Input of this tool is a model-file as generated by ModelCreator or FeatureSelector and a data-file generated by InputReader.
+
+Output of this tool (as specified by '-o') is a text file containing the predicted and, if any, the expected response values in one column each.
+If you would prefer to use molecule files (sdf,mol2,drf) for input and output, please use the tool MolPredictor instead of this one.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,43 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="propertymodifier" name="PropertyModifier" version="0.94">
+    <description>modify molecule property tags</description>
+    <command interpreter="bash"><![CDATA[../../PropertyModifier
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $mode ) != ''  and str( $mode ) != 'None' :
+   -mode "$mode"
+#end if
+#if str( $name ) != ''  and str( $name ) != 'None' :
+   -name "$name"
+#end if
+#if str( $value ) != ''  and str( $value ) != 'None' :
+   -value "$value"
+#end if
+#if str( $new_name ) != ''  and str( $new_name ) != 'None' :
+   -new_name "$new_name"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="mode" label="'delete', 'add' or 'rename' properties" optional="false" type="select">
+            <option value="add">add</option>
+            <option value="rename">rename</option>
+            <option value="delete">delete</option>
+        </param>
+        <param name="name" label="property name ('all' will erase all properties if in delete-mode)" optional="false" area="true" type="text" size="1x15"/>
+        <param name="value" label="property value (in case of prop. adding only)" optional="true" area="true" type="text" size="1x15"/>
+        <param name="new_name" label="new property name (in case of renaming only)" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>With this tools you can add, rename or delete molecule property tags.
+These tags can for example contain information about scores, binding-free-energy, IDs or names for the resp. molecule.
+The output of this tool is a molecule file in which the desired property tags have been added/renamed/deleted (as chosen).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,35 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="propertyplotter" name="PropertyPlotter" version="0.94">
+    <description>plot molecule properties</description>
+    <command interpreter="bash"><![CDATA[../../PropertyPlotter
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $p1 ) != ''  and str( $p1 ) != 'None' :
+   -p1 "$p1"
+#end if
+#if str( $p2 ) != ''  and str( $p2 ) != 'None' :
+   -p2 "$p2"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+-quiet
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="p1" label="name of property 1" optional="false" area="true" type="text" size="1x15"/>
+        <param name="p2" label="name of property 2" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="png"/>
+    </outputs>
+    <help>PropertyPlotter can be used to generate distribution- or scatter-plots of data contained in molecule property-tags.
+
+In case you want to create a scatter-plot, specify the name of both property-tags to be used with '-p1' and '-p2'. If you want to generate a distribution plot, just specify '-p1'.
+The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
+
+The output of this tool is a plot in form of an eps or png-file (as chosen).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,34 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="proteincheck" name="ProteinCheck" version="0.94">
+    <description>quality check for proteins structures</description>
+    <command interpreter="bash"><![CDATA[../../ProteinCheck
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $bc ) != ''  and str( $bc ) != 'None' :
+   -bc
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="bc" label="ignore broken chains" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="pdf"/>
+    </outputs>
+    <help>Check a given protein structure for the following errors:
+    * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
+    * each chain may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments. This test is skipped if the above box is checked.
+    * each atom must have a valid assigned element
+    * the protein must be protonated (since this is necessary for docking/(re-)scoring).
+    * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
+    * there may be no senseless temperature factors (&lt;1 or &gt;100)
+    * there may be no sterical clashes between atoms
+
+A protein structure quality report, containing the results of those tests and a secondary structure prediction, a Ramachandran plot and a temperature factor plot will be generated and saved as a pdf-file.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,29 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="proteinprotonator" name="ProteinProtonator" version="0.94">
+    <description>protonate protein structures</description>
+    <command interpreter="bash"><![CDATA[../../ProteinProtonator
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ph ) != ''  and str( $ph ) != 'None' :
+   -ph "$ph"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="pdb"/>
+        <param name="ph" label="pH-value for pH-dep. protonation" optional="true" type="text" area="true" size="1x5" value="7.0"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="pdb" format_source="i"/>
+    </outputs>
+    <help>ProteinProtonator allows you add hydrogens to a protein structure.
+
+Note that all hydrogen atoms already present in the input file will be ignored. If desired, you can specify a specific pH value, for which protonation is to be done; otherwise a neutral pH will be assumed.
+
+Output of this tool is one pdb-file containing the input protein structure with added hydrogens atoms.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,31 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="rmsdcalculator" name="RMSDCalculator" version="0.94">
+    <description>calculate RMSD between poses</description>
+    <command interpreter="bash"><![CDATA[../../RMSDCalculator
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $org ) != ''  and str( $org ) != 'None' :
+   -org "$org"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+-quiet
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="org" label="molecule file containing the original ('true') poses" optional="false" type="data" format="mol2/sdf/drf"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool calculates the RMSD between different conformations of the same molecule.
+
+Therefore this tool can for example be used to evaluate the different between ligands taken from co-crystal structures and their poses generated by a docking.
+Molecules may be sorted differently in the two input files; a topology hashkey will be used to match molecules to each other.
+
+Output of this tool is a molecule file which will for each molecule contain a property-tag 'RMSD' holding the calculated RMSD value.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,55 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.94">
+    <description>generate ROC or enrichment plots</description>
+    <command interpreter="bash"><![CDATA[../../ScoreAnalyzer
+#if str( $mode ) != ''  and str( $mode ) != 'None' :
+   -mode "$mode"
+#end if
+#if str( $title ) != ''  and str( $title ) != 'None' :
+   -title "$title"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $s ) != ''  and str( $s ) != 'None' :
+   -s "$s"
+#end if
+#if str( $e ) != ''  and str( $e ) != 'None' :
+   -e "$e"
+#end if
+#if str( $t ) != ''  and str( $t ) != 'None' :
+   -t "$t"
+#end if
+#if str( $b ) != ''  and str( $b ) != 'None' :
+   -b
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="mode" label="'roc', 'top50', 'scatter' or 'enrichment'" optional="false" type="select">
+            <option value="roc">roc</option>
+            <option value="top50">top50</option>
+            <option value="scatter">scatter</option>
+            <option value="enrichment">enrichment</option>
+        </param>
+        <param name="title" label="plot title" optional="true" area="true" type="text" size="1x15"/>
+        <param name="s" label="score label" optional="false" area="true" type="text" size="1x15" value="score"/>
+        <param name="e" label="binding-free-energy/class label name" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
+        <param name="t" label="only in case of non-binary act. data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder" optional="true" area="true" type="text" size="1x15"/>
+        <param name="b" label="binary experimental activity data" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="png"/>
+    </outputs>
+    <help>This tool can be used generate plots that allow to evaluate the quality of docking or (re-)scoring.
+
+The type of plot to be generated must be chosen by either '-roc', '-top50', '-scatter' or '-enrichment'. The name of the property-tag that contains the scores to be evaluated (e.g. obtained by docking) is to be specified by '-s'; the name of the property-tag containing experimental data (e.g. binding-free-energy measurements or binder/non-binder info) by use '-e'. If the experimental reference data is not binary, then a threshold below which compound will be considered binders must be given with '-t'.
+The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
+
+The output of this tool is a plot in form of an eps or png-file (as chosen).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,35 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="similarityanalyzer" name="SimilarityAnalyzer" version="0.9">
+    <description>analyze similarity between molecule files</description>
+    <command interpreter="bash"><![CDATA[../../SimilarityAnalyzer
+#if str( $i1 ) != ''  and str( $i1 ) != 'None' :
+   -i1 "$i1"
+#end if
+#if str( $i2 ) != ''  and str( $i2 ) != 'None' :
+   -i2 "$i2"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $title ) != ''  and str( $title ) != 'None' :
+   -title "$title"
+#end if
+-quiet
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i1" label="input molecule file 1" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="i2" label="input molecule file 2" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="title" label="plot title" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="png"/>
+    </outputs>
+    <help>This tool evaluates the similarity between molecules in two input files and creates a distribution plot to visualize the result.
+
+Therefore, for each molecule a pathway-based, hashed binary fingerprint is generated and compared to the fingerprint of other molecules by use of the Tanimoto similarity measure.
+The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
+
+The resulting plot (in form of an eps-, png- or pdf-file; as chosen) shows the distribution of similarity values obtained by comparing each molecule in input file 1 against each molecule in input file 2.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,49 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="simplerescorer" name="SimpleRescorer" version="0.94">
+    <description>rescore docking results</description>
+    <command interpreter="bash"><![CDATA[../../SimpleRescorer
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $function ) != ''  and str( $function ) != 'None' :
+   -function "$function"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+        <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="function" label="scoring function: 'MM', 'PLP' or 'PB'" optional="true" type="select">
+            <option value="MM">MM</option>
+            <option value="PLP">PLP</option>
+            <option value="PB">PB</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool rescores docking output poses.
+A scoring function is used to evaluate the binding-free-energy of each compound. This is similar to the scoring done during docking; details depend on the config-file (if one is specified).
+
+As input we need:
+    * a file containing a protonated protein in pdb-format
+    * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+    * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein.
+
+Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,45 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.94">
+    <description>define spatial constraint</description>
+    <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $type ) != ''  and str( $type ) != 'None' :
+   -type "$type"
+#end if
+#if str( $n ) != ''  and str( $n ) != 'None' :
+   -n "$n"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="ini" label="input configuration file" optional="true" type="data" format="ini"/>
+        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="type" label="'fraction' or 'number' of compound atoms" optional="false" type="select">
+            <option value="fraction">fraction</option>
+            <option value="number">number</option>
+        </param>
+        <param name="n" label="desired number/fraction of atoms in spatial area" optional="false" type="text" area="true" size="1x5" value=""/>
+        <param name="p" label="penalty value" optional="false" type="text" area="true" size="1x5" value="1e11"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="ini"/>
+    </outputs>
+    <help>This tool allows to define spatial constraints for docking or scoring.
+
+For convenience, we use a molecule file as input and generate a boundary box around the contained compound. This molecule can therefore for example contain the reference ligand (obtained from a co-crystal structure), or a docked compound, or just a set of dummy atoms used to manually define the boundaries of the desired spatial constraint.
+Furthermore, you need to specify how many atoms of the compound to be docked (or scored) should be located inside the spatial area. You can either specify a number of atoms or a fraction of molecule atoms for this.
+
+Output of this tool is a ini-file that contains the desired spatial constraint.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,61 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="tagres-train" name="TaGRes-train" version="0.94">
+    <description>Target-specific Grid-Rescoring, training</description>
+    <command interpreter="bash"><![CDATA[../../TaGRes-train
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $method ) != ''  and str( $method ) != 'None' :
+   -method "$method"
+#end if
+#if str( $function ) != ''  and str( $function ) != 'None' :
+   -function "$function"
+#end if
+#if str( $exp ) != ''  and str( $exp ) != 'None' :
+   -exp "$exp"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+        <param name="i" label="training compound data set" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select">
+            <option value="Rescoring3D">Rescoring3D</option>
+            <option value="Rescoring4D">Rescoring4D</option>
+            <option value="Rescoring1D">Rescoring1D</option>
+        </param>
+        <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select">
+            <option value="MM">MM</option>
+            <option value="PLP">PLP</option>
+        </param>
+        <param name="exp" label="property-tag name containing experimentally determined binding-free-energies" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mod"/>
+    </outputs>
+    <help>This tool generates a model for Target-specific Grid-Rescoring (TaGRes).
+As input we need:
+
+    * a file containing a protonated protein in pdb-format
+    * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+    * a file containing a training data set, i.e. compounds whose binding-free-energy to the specified target is known and annotated in this file. Those compounds should have been docked into the specified protein.
+
+A scoring function is applied and an interaction-grid thereby generated for each input compound. Together with the known binding-free-energy, those grids are used to automatically search for the best linear or non-linear regression model that can approximate the binding-free-energy. After this model has been generated, you can pass it to the tool TaGRes and rescore (different) compounds with it.
+
+The output of this TaGRes-train is a file that contains the generated regression model. However, if no model with suitable prediction quality was found, an error will be shown and no model-file will be written.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/TaGRes.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,63 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="tagres" name="TaGRes" version="0.94">
+    <description>Target-specific Grid-Rescoring</description>
+    <command interpreter="bash"><![CDATA[../../TaGRes
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $mod ) != ''  and str( $mod ) != 'None' :
+   -mod "$mod"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $method ) != ''  and str( $method ) != 'None' :
+   -method "$method"
+#end if
+#if str( $function ) != ''  and str( $function ) != 'None' :
+   -function "$function"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+        <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="mod" label="model-file generated by TaGRes-train" optional="false" type="data" format="data"/>
+        <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select">
+            <option value="Rescoring3D">Rescoring3D</option>
+            <option value="Rescoring4D">Rescoring4D</option>
+            <option value="Rescoring1D">Rescoring1D</option>
+        </param>
+        <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select">
+            <option value="MM">MM</option>
+            <option value="PLP">PLP</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool rescores docking output poses using Target-specific Grid-Rescoring.
+Please generate a regression model for binding-affinity approximation for your protein target by use of the tool TaGRes-train before using this tool.
+As input TaGRes needs:
+
+    * a file containing a protonated protein in pdb-format
+    * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+    * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein.
+    * a regression model file as generated by TaGRes-train for same protein target than the one specified here.
+
+TaGRes will evaluate each given input pose with a scoring function and apply the specified regression model to the score contributions generated this way, resulting in a re-score value, i.e. a (probably) enhanced approximation of the compound's binding-free-energy.
+
+Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Validator.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,36 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="validator" name="Validator" version="1.1">
+    <description>evaluate quality of a QSAR model</description>
+    <command interpreter="bash"><![CDATA[../../Validator
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $dat ) != ''  and str( $dat ) != 'None' :
+   -dat "$dat"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $type ) != ''  and str( $type ) != 'None' :
+   -type "$type"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input mod-file" optional="false" type="data" format="mod"/>
+        <param name="dat" label="data-file" optional="false" type="data" format="dat"/>
+        <param name="type" label="feature-selection type" optional="false" type="select">
+            <option value="cross validation">cross validation</option>
+            <option value="bootstrapping">bootstrapping</option>
+            <option value="response permutation">response permutation</option>
+            <option value="evaluate fit to test data">evaluate fit to test data</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="o" format="txt"/>
+    </outputs>
+    <help>Validator evaluates the quality of a QSAR model.
+
+The validation technique to be used for this can selected by '-type'. As input this tools need a model-file as generate by InputReader or FeatureSelector and a data-file generated by InputReader containing the prediction data set. Note that the latter must contain response values so that predictions done by the supplied model can be compared to those values by the validation method.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/VendorFinder.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,49 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="vendorfinder" name="VendorFinder" version="0.94">
+    <description>search vendors for compounds</description>
+    <command interpreter="bash"><![CDATA[../../VendorFinder
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $d ) != ''  and str( $d ) != 'None' :
+   -d "$d"
+#end if
+#if str( $u ) != ''  and str( $u ) != 'None' :
+   -u "$u"
+#end if
+#if str( $h ) != ''  and str( $h ) != 'None' :
+   -h "$h"
+#end if
+#if str( $port ) != ''  and str( $port ) != 'None' :
+   -port "$port"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $opt ) != ''  and str( $opt ) != 'None' :
+   -opt
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file containing compounds" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/>
+        <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/>
+        <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/>
+        <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/>
+        <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/>
+        <param name="opt" label="optimize purchase, i.e. select cheapest sources and sort by vendor" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="txt"/>
+    </outputs>
+    <help>This tool can be used to fetch information about vendors for each compound in the given input file from a data base.
+
+Of course, vendors can only be found if they have been stored in the database that is to be used here. Use DBImporter with molecules files obtained from the compound vendors of your choice in order to create such a database.
+
+Output of this tool is a text-file containing a list of vendor-name and vendor's compound-ID for each compound in the input file for which vendor-information was found in the database.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/WaterFinder.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,55 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="waterfinder" name="WaterFinder" version="0.94">
+    <description>find strongly bound waters</description>
+    <command interpreter="bash"><![CDATA[../../WaterFinder
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $wat ) != ''  and str( $wat ) != 'None' :
+   -wat "$wat"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ai ) != ''  and str( $ai ) != 'None' :
+   -ai
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+        <param name="wat" label="input pdb-file containing water molecules (if not part of rec.-file)" optional="true" type="data" format="pdb"/>
+        <param name="ai" label="use ab-initio water search (ignore water in pdb-file), experimental!" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="pdb"/>
+    </outputs>
+    <help>This tool searches for crystal waters that
+    * either interact very strongly with the receptor
+    * or that interact strongly with receptor and reference ligand,
+      thus functioning as a water bridge.
+
+Water molecules in the pdb-structure (i.e. single oxygens) are automatically protonated and rotationally optimized before the search is done.
+
+As input we need:
+    * a file containing a protonated protein in pdb-format.
+      This file should contain water molecules that are to be evaluated by this tool.
+      However, you can also use a separate pdb-file as input for the water molecules (see below).
+    * a file containing a reference ligand.
+      This reference ligand should be located in the binding pocket.
+      Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+    * optionally a file in pdb-format containing water molecules.
+      If you specify such a file , all water molecules appearing in the
+      protein input-file (if any) will be ignored.
+
+Output of this tool is a pdb-file containing the protein and all detected strongly bound water molecules.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/upload.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,46 @@
+<?xml version="1.0"?>
+
+<tool name="Upload File" id="cadds_upload" version="1.1.2">
+  <description>
+    from your computer
+  </description>
+  <action module="galaxy.tools.actions.upload" class="UploadToolAction"/>
+  <command interpreter="python">
+      ../../../data_source/upload.py $GALAXY_ROOT_DIR $GALAXY_DATATYPES_CONF_FILE $paramfile
+    #set $outnum = 0
+    #while $varExists('output%i' % $outnum):
+        #set $output = $getVar('output%i' % $outnum)
+        #set $outnum += 1
+        ${output.dataset.dataset.id}:${output.files_path}:${output}
+    #end while
+  </command>
+  <inputs nginx_upload="true">
+    <param name="file_type" type="select" label="File Format" help="Which format? See help below">
+      <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ &quot;%s%s%s&quot; % ( line, self.separator, line ) for line in obj ]">
+        <column name="value" index="1"/>
+        <column name="name" index="0"/>
+        <filter type="sort_by" column="0"/>
+        <filter type="add_value" name="Auto-detect" value="auto" index="0"/>
+      </options>
+    </param>
+    <param name="async_datasets" type="hidden" value="None"/>
+    <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata">
+      <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: For NGS and other large files (>~2GB), uploading via HTTP/FTP URL (below) is the most reliable method.">
+        <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator> <!-- use validator to post message to user about needing to reselect the file, since most browsers won't accept the value attribute for file inputs -->
+      </param>
+      <param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/>
+      <param name="ftp_files" type="ftpfile" label="Files uploaded via FTP"/>
+      <!--
+      <param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand.">
+        <option value="Yes">Yes</option>
+      </param>
+      -->
+    </upload_dataset>
+    <!--<param name="dbkey" type="genomebuild" label="Genome" />-->
+    <conditional name="files_metadata" title="Specify metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" />
+    <!-- <param name="other_dbkey" type="text" label="Or user-defined Genome" /> -->
+  </inputs>
+  <help>
+
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/install.sh	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,84 @@
+#!/bin/bash
+
+QT_DIR=""
+INSTALL_DIR=""
+#OPT="Linux_x86_64"
+
+
+checkDir()
+{
+	echo -n "checking for "$1" ... "
+	if [ -f $QT_DIR/$1 ]; then
+		echo $QT_DIR/$1
+		return 1
+	else
+		echo "not found!"
+		return 0
+	fi
+}
+
+echo
+cat license.txt
+echo
+echo -n "Do you agree to this license?! (y/n) "
+read license_accepted
+echo
+
+if [ "$license_accepted" != "y" ] && [ "$license_accepted" != "yes" ]; then
+	echo "License was not accepted, aborting."
+	exit 1
+fi
+
+echo -n "Please enter *absolute* path to install target-directory: "
+
+read INSTALL_DIR
+if [ ! -d $INSTALL_DIR ]; then
+	mkdir $INSTALL_DIR
+fi
+
+if [ ! -d $INSTALL_DIR ]; then
+	echo
+	echo "[Error:] The desired install-directory does not exist and could also not be created!"
+	echo "Perhaps there was a typo or you do not have permission to create this folder."
+	echo "Aborting install."
+	echo
+	exit 1
+fi
+
+# if [ -f /usr/lib/libQtCore.so.4 ] && [ -f  /usr/lib/libQtGui.so.4 ]; then
+# 	QT_DIR=/usr/lib
+# else
+# 	echo "Please enter absolute path to the directory containing"
+# 	echo -n "your Qt4 libraries (version>=4.3.5): "
+# 	read QT_DIR
+# fi
+
+# checkDir libQtCore.so.4; ok=$?;
+# checkDir libQtGui.so.4;  if [ $ok = 1 ]; then let ok $?; fi
+# #checkDir libQtOpenGL.so; if [ $ok = 1 ]; then ok=$?; fi
+#
+# if [ $ok != 1 ]; then
+# 	echo "Aborting installation due to missing Qt4!"
+# 	exit 1
+# fi
+
+cd bin
+programs=`ls *.bin`
+cd ..
+for i in $programs; do
+	chmod +x ${i:0:${#i}-4}
+done
+
+
+mv * $INSTALL_DIR/
+
+if [ -f $INSTALL_DIR/CADDSuite-description.txt ]; then
+	echo
+	echo
+	cat $INSTALL_DIR/CADDSuite-description.txt
+fi
+
+echo
+echo "Installation finished."
+echo "You can find all installed programs in $INSTALL_DIR."
+echo
Binary file CADDSuite/lib/Accelerate has changed
Binary file CADDSuite/lib/QtCore has changed
Binary file CADDSuite/lib/QtNetwork has changed
Binary file CADDSuite/lib/QtSql has changed
Binary file CADDSuite/lib/QtXml has changed
Binary file CADDSuite/lib/libBALL.1.4.dylib has changed
Binary file CADDSuite/lib/libBLAS.dylib has changed
Binary file CADDSuite/lib/libSystem.B.dylib has changed
Binary file CADDSuite/lib/libboost_iostreams.dylib has changed
Binary file CADDSuite/lib/libboost_regex.dylib has changed
Binary file CADDSuite/lib/libboost_system.dylib has changed
Binary file CADDSuite/lib/libboost_thread.dylib has changed
Binary file CADDSuite/lib/libgsl.0.dylib has changed
Binary file CADDSuite/lib/libgslcblas.0.dylib has changed
Binary file CADDSuite/lib/libmysqlclient.18.dylib has changed
Binary file CADDSuite/lib/libopenbabel.4.dylib has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/license.txt	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,20 @@
+-------------------------------------------------------------------------------
+   CADDSuite - A flexible and open framework and workflow system
+               for computer-aided drug design
+-------------------------------------------------------------------------------
+
+Copyright (C) 2011  Marcel Schumann
+
+CADDSuite is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 3 of the License, or (at
+your option) any later version.
+
+CADDSuite is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, see <http://www.gnu.org/licenses/>.
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/rescoring_common	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/rescoring_common.bin "$@"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/setPathes.sh	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,10 @@
+#!/bin/bash
+export LD_LIBRARY_PATH="$BASE_DIR"/lib
+export DYLD_LIBRARY_PATH="$BASE_DIR"/lib
+export BALL_DATA_PATH="$BASE_DIR"/data
+export BABEL_DATADIR="$BASE_DIR"/data/OpenBabel/
+export QT_PLUGIN_PATH="$BASE_DIR"/lib/plugins/
+export PATH="$BASE_DIR"/bin:$PATH
+export GDFONTPATH="$BASE_DIR"/data/fonts
+export GNUPLOT_DEFAULT_GDFONT=FreeSans
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/suite_config.xml	Sun Jun 26 14:01:09 2011 -0400
@@ -0,0 +1,141 @@
+<suite id="CADDSuite_toolsuite" name="CADDSuite" version="0.94">
+
+<description>
+CADDSuite: A flexible and open framework for Computer-Aided Drug Design
+</description>
+<tool id="cadds_upload" name="Upload File" version="1.1.2">
+    <description>from your computer</description>
+</tool>
+
+<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.94">
+    <description>rescore w/ anti-target dock-results</description>
+</tool>
+<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.94">
+    <description>fix bindingdb.org downloads</description>
+</tool>
+<tool id="combilibgenerator" name="CombiLibGenerator" version="0.94">
+    <description>generate combinatorial lib</description>
+</tool>
+<tool id="constraintsfinder" name="ConstraintsFinder" version="0.94">
+    <description>find strongly interacting residues</description>
+</tool>
+<tool id="converter" name="Converter" version="0.94">
+    <description>interconvert molecular file-formats</description>
+</tool>
+<tool id="dbexporter" name="DBExporter" version="0.94 (ob)">
+    <description>export molecules from data base</description>
+</tool>
+<tool id="dbimporter" name="DBImporter" version="0.94 (ob)">
+    <description>import molecules into data base</description>
+</tool>
+<tool id="dockresultmerger" name="DockResultMerger" version="0.94">
+    <description>merge docking output files</description>
+</tool>
+<tool id="evensplit" name="EvenSplit" version="0.94">
+    <description>generate splits w/ equal property range</description>
+</tool>
+<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.94">
+    <description>generate galaxy tool-config files</description>
+</tool>
+<tool id="gridbuilder" name="GridBuilder" version="0.94">
+    <description>create score-grids for docking</description>
+</tool>
+<tool id="imeedydock" name="IMGDock" version="0.94">
+    <description>Iterative Multi-Greedy Docking</description>
+</tool>
+<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.94">
+    <description>define interaction constraint</description>
+</tool>
+<tool id="ligcheck" name="LigCheck" version="0.94">
+    <description>check molecules for errors</description>
+</tool>
+<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.94">
+    <description>generate 3D coordinates for small molecules</description>
+</tool>
+<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.94">
+    <description>split molecule files</description>
+</tool>
+<tool id="molcombine" name="MolCombine" version="0.94">
+    <description>combine molecular files</description>
+</tool>
+<tool id="moldepict" name="MolDepict" version="0.94">
+    <description>create structure diagrams</description>
+</tool>
+<tool id="molfilter" name="MolFilter" version="0.9">
+    <description>filter molecule files</description>
+</tool>
+<tool id="pdbcutter" name="PDBCutter" version="0.94">
+    <description>separate ligand and receptor</description>
+</tool>
+<tool id="pdbdownload" name="PDBDownload" version="0.94">
+    <description>retrieve pdb-file from pdb.org</description>
+</tool>
+<tool id="partialchargescopy" name="PartialChargesCopy" version="0.94">
+    <description>transfer part. charges between files</description>
+</tool>
+<tool id="pocketdetector" name="PocketDetector" version="0.94">
+    <description>detect binding pocket</description>
+</tool>
+<tool id="propertymodifier" name="PropertyModifier" version="0.94">
+    <description>modify molecule property tags</description>
+</tool>
+<tool id="propertyplotter" name="PropertyPlotter" version="0.94">
+    <description>plot molecule properties</description>
+</tool>
+<tool id="proteincheck" name="ProteinCheck" version="0.94">
+    <description>quality check for proteins structures</description>
+</tool>
+<tool id="proteinprotonator" name="ProteinProtonator" version="0.94">
+    <description>protonate protein structures</description>
+</tool>
+<tool id="rmsdcalculator" name="RMSDCalculator" version="0.94">
+    <description>calculate RMSD between poses</description>
+</tool>
+<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.94">
+    <description>generate ROC or enrichment plots</description>
+</tool>
+<tool id="similarityanalyzer" name="SimilarityAnalyzer" version="0.9">
+    <description>analyze similarity between molecule files</description>
+</tool>
+<tool id="simplerescorer" name="SimpleRescorer" version="0.94">
+    <description>rescore docking results</description>
+</tool>
+<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.94">
+    <description>define spatial constraint</description>
+</tool>
+<tool id="tagres-train" name="TaGRes-train" version="0.94">
+    <description>Target-specific Grid-Rescoring, training</description>
+</tool>
+<tool id="tagres" name="TaGRes" version="0.94">
+    <description>Target-specific Grid-Rescoring</description>
+</tool>
+<tool id="vendorfinder" name="VendorFinder" version="0.94">
+    <description>search vendors for compounds</description>
+</tool>
+<tool id="waterfinder" name="WaterFinder" version="0.94">
+    <description>find strongly bound waters</description>
+</tool>
+<tool id="automodel" name="AutoModel" version="1.1">
+    <description>automatically find best QSAR model</description>
+</tool>
+<tool id="featureselector" name="FeatureSelector" version="1.1">
+    <description>run feature-selection on a QSAR model</description>
+</tool>
+<tool id="inputpartitioner" name="InputPartitioner" version="1.1">
+    <description>split QSAR data set</description>
+</tool>
+<tool id="inputreader" name="InputReader" version="1.1">
+    <description>generate QSAR data set</description>
+</tool>
+<tool id="modelcreator" name="ModelCreator" version="1.1">
+    <description>create a QSAR model</description>
+</tool>
+<tool id="molpredictor" name="MolPredictor" version="1.1">
+    <description>predict molecule activities with QSAR model</description>
+</tool>
+<tool id="predictor" name="Predictor" version="1.1">
+    <description>predict activities with QSAR model</description>
+</tool>
+<tool id="validator" name="Validator" version="1.1">
+    <description>evaluate quality of a QSAR model</description>
+</tool></suite>